diff --git a/RE_sites.py b/RE_sites.py
index 130a93b..0829136 100755
--- a/RE_sites.py
+++ b/RE_sites.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python2
+#!/usr/bin/env python
 import re 
 import sys
 import argparse
@@ -11,7 +11,7 @@ def parse_fasta(fh):
         if ln[0] == '>':
             # check for bad name
             if ":" in ln:
-                print >> sys.stderr, "Error, your fasta records contain a ':' (%s). SALSA requires fasta to not contain this character, please update your fasta and re-try"%(ln[1:].rstrip())
+                print("Error, your fasta records contain a ':' (%s). SALSA requires fasta to not contain this character, please update your fasta and re-try"%(ln[1:].rstrip()), file=sys.stderr)
                 sys.exit(1)
 
             # new name line; remember current sequence's short name
@@ -22,7 +22,7 @@ def parse_fasta(fh):
             # append nucleotides to current sequence
             fa[current_short_name].append(ln.rstrip())
     # Part 2: join lists into strings
-    for short_name, nuc_list in fa.iteritems():
+    for short_name, nuc_list in fa.items():
         # join this sequence's lines into one long string
         fa[short_name] = ''.join(nuc_list)
     return fa
@@ -39,14 +39,14 @@ def main():
     if args.enzyme == "DNASE":
         for key in f:
             id, seq = key, f[key]
-            print id, len(seq)/2, len(seq)/2
+            print(id, len(seq)/2, len(seq)/2)
         sys.exit(0)
 
     enzymes_input = args.enzyme.replace(' ','').split(',')
     final_enzymes = []
     for each in enzymes_input:
         if not re.match("^[ACGTN]+$", each):
-            print >> sys.stderr, "Error, enzyme should be restriction site sequence (e.g. AACTT) not enzyme name or DNASE, you input %s"%(each)
+            print("Error, enzyme should be restriction site sequence (e.g. AACTT) not enzyme name or DNASE, you input %s"%(each), file=sys.stderr)
             sys.exit(1)
 
         if 'N' in each:
@@ -85,7 +85,7 @@ def main():
         #     else:
         #         rigt_count += 1
 
-        print id, left_count, rigt_count
+        print(id, left_count, rigt_count)
 
     
 
diff --git a/alignments2txt.py b/alignments2txt.py
index a2c6be4..3af751c 100755
--- a/alignments2txt.py
+++ b/alignments2txt.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python2
+#!/usr/bin/env python
 import os,sys
 import argparse
 import pickle
@@ -48,7 +48,7 @@ def update_bed(expanded_scaffold):
         path = expanded_scaffold[key]
         scaffold_length[key] = 0
         offset = 0
-        for i in xrange(0,len(path)-1,2):
+        for i in range(0,len(path)-1,2):
             contig = path[i].split(':')[0]
             contig2scaffold[contig] = key
             ori = path[i].split(':')[1] + path[i+1].split(':')[1]
@@ -117,7 +117,7 @@ def update_bed(expanded_scaffold):
                             #o_lines += curr_scaffold+'\t'+str(new_curr_start)+'\t'+str(new_curr_end)+'\t'+curr_attrs[3]+'\n'
                             count += 1
                             if count == 1000000:
-                                print olines
+                                print(olines)
                                 #output.write(o_lines)
                                 count = 0
                                 olines = ""
@@ -125,7 +125,7 @@ def update_bed(expanded_scaffold):
                 prev_line = line
 
             #write remaining lines
-            print olines
+            print(olines)
             #output.write(o_lines)
             #output.close()
 
diff --git a/correct.py b/correct.py
index 88421e3..ab42e00 100755
--- a/correct.py
+++ b/correct.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python2
+#!/usr/bin/env python
 import sys
 
 #reads input assembly, breakpoints given by the method and outputs new contig file with lengths
@@ -18,7 +18,7 @@ def parse_fasta(fh):
             # append nucleotides to current sequence
             fa[current_short_name].append(ln.rstrip())
     # Part 2: join lists into strings
-    for short_name, nuc_list in fa.iteritems():
+    for short_name, nuc_list in fa.items():
         # join this sequence's lines into one long string
         fa[short_name] = ''.join(nuc_list)
     return fa
@@ -94,7 +94,7 @@ def parse_fasta(fh):
 ofasta = open(sys.argv[4]+'/asm.cleaned.fasta','w')
 for seq in contig2newseq:
     contig_seq = contig2newseq[seq]
-    chunks = [contig_seq[i:i+80] for i in xrange(0,len(contig_seq),80)]
+    chunks = [contig_seq[i:i+80] for i in range(0,len(contig_seq),80)]
     ofasta.write('>'+seq+'\n')
     for chunk in chunks:
         ofasta.write(chunk+'\n')
diff --git a/fast_scaled_scores.py b/fast_scaled_scores.py
index cfb9c87..35ecb2d 100755
--- a/fast_scaled_scores.py
+++ b/fast_scaled_scores.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python2
+#!/usr/bin/env python
 import networkx as nx
 import sys
 import argparse
diff --git a/get_seq.py b/get_seq.py
index 8484298..e92a429 100755
--- a/get_seq.py
+++ b/get_seq.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python2
+#!/usr/bin/env python
 import pickle
 import argparse
 
@@ -16,7 +16,7 @@ def parse_fasta(fh):
             # append nucleotides to current sequence
             fa[current_short_name].append(ln.rstrip())
     # Part 2: join lists into strings
-    for short_name, nuc_list in fa.iteritems():
+    for short_name, nuc_list in fa.items():
         # join this sequence's lines into one long string
         fa[short_name] = ''.join(nuc_list)
     return fa
@@ -30,7 +30,7 @@ def parse_fasta(fh):
 args = parser.parse_args()
 
 revcompl = lambda x: ''.join([{'A':'T','B':'N','C':'G','G':'C','T':'A','N':'N','R':'N','M':'N','Y':'N','S':'N','W':'N','K':'N','a':'t','c':'g','g':'c','t':'a','n':'n',' ':'',}[B] for B in x][::-1])
-scaff_map = pickle.load(open(args.map,'r'))
+scaff_map = pickle.load(open(args.map,'rb'))
 
 contig_length = {}
 id2seq = {}
@@ -46,11 +46,11 @@ def parse_fasta(fh):
 for scaffold in scaff_map:
 	path = scaff_map[scaffold]
 	length = 0
-	for i in xrange(0,len(path)-1,2):
+	for i in range(0,len(path)-1,2):
 		length += contig_length[path[i].split(':')[0]]
 	scaff2length[scaffold] = length
 
-sorted_scaffolds = sorted(scaff2length.items(), key=lambda x: x[1],reverse=True)
+sorted_scaffolds = sorted(list(scaff2length.items()), key=lambda x: x[1],reverse=True)
 
 c_id = 1
 line = ""
@@ -114,7 +114,7 @@ def parse_fasta(fh):
     # rec = SeqRecord(Seq(curr_contig,generic_dna),id='scaffold_'+str(c_id))
     # recs.append(rec)
     # print c_id
-    chunks = [curr_contig[i:i+80] for i in xrange(0,len(curr_contig),80)]
+    chunks = [curr_contig[i:i+80] for i in range(0,len(curr_contig),80)]
     ofile.write('>scaffold_'+str(c_id)+'\n')
     for chunk in chunks:
         ofile.write(chunk+'\n')
diff --git a/layout_unitigs.py b/layout_unitigs.py
index b6a4bb5..820e33e 100755
--- a/layout_unitigs.py
+++ b/layout_unitigs.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python2
+#!/usr/bin/env python
 import networkx as nx
 import sys
 import operator
@@ -177,7 +177,7 @@ def load_unitig_mapping():
                     unitig_graph.add_edge(curr_unitig+':E',prev_unitig+':E')
 
             prev_line = line
-    print >> sys.stderr, 'Unitig tiling graph loaded, nodes = ' + str(len(unitig_graph.nodes())) + ' edges = ' + str(len(unitig_graph.edges()))
+    print('Unitig tiling graph loaded, nodes = ' + str(len(unitig_graph.nodes())) + ' edges = ' + str(len(unitig_graph.edges())), file=sys.stderr)
     return unitig_graph
 
 
@@ -219,7 +219,7 @@ def load_tenx_graph(cutoff):
 contig2scaffold = {}
 if int(args.iteration) > 1:
     try:
-        previous_scaffolds = pickle.load(open(args.directory+'/scaffolds_iteration_'+str(iteration-1)+'.p','r'))
+        previous_scaffolds = pickle.load(open(args.directory+'/scaffolds_iteration_'+str(iteration-1)+'.p','rb'))
         for key in previous_scaffolds:
             contigs_1 = previous_scaffolds[key]
             first = contigs_1[0].split(':')[0]
@@ -240,7 +240,7 @@ def load_tenx_graph(cutoff):
 
 
 #Load the best score graph first, keep log of used and unused links
-print >> sys.stderr,  'Loading Hi-C links '
+print('Loading Hi-C links ', file=sys.stderr)
 '''
 Counts to keep log of each types of edge loaded in the graph
 '''
@@ -257,11 +257,11 @@ def test_edge(scaffold_first,scaffold_second,G_test,type):
     last_first = scaffold_first[-1]
     first_second = scaffold_second[0]
     last_second = scaffold_second[-1]
-    print 'testing'
-    print first_first
-    print first_second
-    print last_first
-    print last_second
+    print('testing')
+    print(first_first)
+    print(first_second)
+    print(last_first)
+    print(last_second)
     if G_test.has_edge(last_first,first_second):
         v1 = c1+':E'
         v2 = c2 +':B'
@@ -579,8 +579,8 @@ def generate_scaffold_graph():
     for ctg in list(contigs):
         G.add_edge(ctg+":B", ctg+":E", t="c", score=0, linktype='implicit')
 
-    print >> sys.stderr, 'Hybrid scaffold graph loaded, nodes = ' + str(len(G.nodes())) + ' edges = ' + str(len(G.edges()))
-    print >> sys.stderr, 'Hi-C implied edges = ' + str(hic_edges)
+    print('Hybrid scaffold graph loaded, nodes = ' + str(len(G.nodes())) + ' edges = ' + str(len(G.edges())), file=sys.stderr)
+    print('Hi-C implied edges = ' + str(hic_edges), file=sys.stderr)
 
 
 '''
@@ -592,7 +592,8 @@ def get_seed_scaffold():
     seed_scaffolds = {} #this stores initial long scaffolds
     to_merge = set()
 
-    for subg in nx.connected_component_subgraphs(G):
+    #for subg in nx.connected_component_subgraphs(G):
+    for subg in (G.subgraph(c) for c in nx.connected_components(G)):
         p = []
         for node in subg.nodes():
             if subg.degree(node) == 1:
@@ -664,7 +665,7 @@ def insert(assignment, seed_scaffolds):
         orientation = ''
         pos = -1
         #first check at all middle positions
-        for i in xrange(1,len(path)-1,2):
+        for i in range(1,len(path)-1,2):
             score_fow = -1
             score_rev = -1
             if all_G.has_edge(five_prime,path[i]) and all_G.has_edge(three_prime,path[i+1]):
@@ -722,7 +723,7 @@ def update_bed(expanded_scaffold):
         path = expanded_scaffold[key]
         scaffold_length[key] = 0
         offset = 0
-        for i in xrange(0,len(path),2):
+        for i in range(0,len(path),2):
             contig = path[i].split(':')[0]
             contig2scaffold[contig] = key
             ori = path[i].split(':')[1] + path[i+1].split(':')[1]
@@ -735,7 +736,7 @@ def update_bed(expanded_scaffold):
 
     scaffold_re = {}
     for key in expanded_scaffold:
-        print key
+        print(key)
         path = expanded_scaffold[key]
         length = scaffold_length[key]
         offset = 0
@@ -751,7 +752,7 @@ def update_bed(expanded_scaffold):
                 scaffold_re[key] = (right,left)
         else:
             midpoint = length/2
-            for i in xrange(0,len(path),2):
+            for i in range(0,len(path),2):
                 contig = path[i].split(':')[0]
                 contig2scaffold[contig] = key
                 left,right = re_counts[contig]
@@ -915,7 +916,8 @@ def merge(contigs):
 
     #print best_hic_graph.nodes()
 
-    for g in nx.connected_component_subgraphs(best_hic_graph):
+    #for g in nx.connected_component_subgraphs(best_hic_graph):
+    for g in (best_hic_graph.subgraph(c) for c in nx.connected_components(best_hic_graph)):
         #print g.nodes()
         p = []
         for node in g.nodes():
@@ -983,7 +985,7 @@ def correct_scaffolds(curr_scaffolds):
     path = final_scaffolds[key]
     new_path = []
     #print path
-    for i in xrange(0,len(path)-1,2):
+    for i in range(0,len(path)-1,2):
         #print path
         contig = path[i].split(':')[0]
         scaffolded_contigs[contig] = True
@@ -1010,7 +1012,7 @@ def correct_scaffolds(curr_scaffolds):
     oline = ''
     oline += 'scaffold_'+str(key) +'\t'
     cum_len = 0
-    for i in xrange(0,len(path)-1,2):
+    for i in range(0,len(path)-1,2):
         #print path
         contig = path[i].split(':')[0]
         cum_len += prev_len[contig]
@@ -1095,7 +1097,7 @@ def correct_scaffolds(curr_scaffolds):
 
 # expanded_scaffold_paths = updated_scaffolds
 
-pickle.dump(expanded_scaffold_paths,open(args.directory+'/scaffolds_iteration_'+str(args.iteration)+'.p','w'))
+pickle.dump(expanded_scaffold_paths,open(args.directory+'/scaffolds_iteration_'+str(args.iteration)+'.p','wb'))
 update_bed(expanded_scaffold_paths)
 
 
diff --git a/make_links.py b/make_links.py
index 26c3e07..fe10a34 100755
--- a/make_links.py
+++ b/make_links.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python2
+#!/usr/bin/env python
 import operator
 import math
 import sys
@@ -55,7 +55,7 @@ def main():
     coordinates_map = {}
     first_in_pair = {}
     second_in_pair = {}
-    print >> sys.stderr, 'bedfile started'
+    print('bedfile started', file=sys.stderr)
     prev_line = ''
     with open(args.mapping,'r') as f:
         for line in f:
@@ -78,8 +78,8 @@ def main():
                 if prev_read.split('/')[0] == curr_read.split('/')[0]:
                     #print 'here'
 
-                    pos1 = (long(prev_attrs[1]) + long(prev_attrs[2]))/2.0
-                    pos2 = (long(attrs[1]) + long(attrs[2]))/2.0
+                    pos1 = (int(prev_attrs[1]) + int(prev_attrs[2]))/2.0
+                    pos2 = (int(attrs[1]) + int(attrs[2]))/2.0
                     # l1 = 300000.0
                     # l2 = 300000.0
                     #print pos1, pos2
@@ -152,11 +152,11 @@ def main():
             #     continue
 
 
-    print >> sys.stderr, 'bedfile loaded'
+    print('bedfile loaded', file=sys.stderr)
 
 
 
-    print len(contig_links)
+    print(len(contig_links))
     ofile = open(args.directory+'/contig_links_iteration_'+str(iteration),'w')
     for key in contig_links:
         if key != '':
diff --git a/refactor_breaks.py b/refactor_breaks.py
index 109e0a4..df10c1a 100755
--- a/refactor_breaks.py
+++ b/refactor_breaks.py
@@ -10,7 +10,7 @@
 
 iteration = int(args.iteration)
 breakpoints = {}
-scaffolds_current = pickle.load(open(args.directory+'/scaffolds_iteration_'+str(iteration-1)+'.p','r'))
+scaffolds_current = pickle.load(open(args.directory+'/scaffolds_iteration_'+str(iteration-1)+'.p','rb'))
 
 with open(args.directory+'/misasm_iteration_'+args.iteration+'.report','r') as f:
     for line in f:
@@ -22,7 +22,7 @@
             if len(attrs) < 2:
                 continue
             breakpoints[attrs[0]] = []
-            for i in xrange(1,len(attrs)):
+            for i in range(1,len(attrs)):
                 breakpoints[attrs[0]].append(int(attrs[i]))
         except:
             continue
@@ -49,7 +49,7 @@ def update_bed(expanded_scaffold):
         path = expanded_scaffold[key]
         scaffold_length[key] = 0
         offset = 0
-        for i in xrange(0,len(path)-1,2):
+        for i in range(0,len(path)-1,2):
             contig = path[i].split(':')[0]
             contig2scaffold[contig] = key
             ori = path[i].split(':')[1] + path[i+1].split(':')[1]
@@ -77,7 +77,7 @@ def update_bed(expanded_scaffold):
                 scaffold_re[key] = (right,left)
         else:
             midpoint = length/2
-            for i in xrange(0,len(path),2):
+            for i in range(0,len(path),2):
                 contig = path[i].split(':')[0]
                 left,right = re_counts[contig]
                 curr_contig_start = contig2info[contig][0]
@@ -218,7 +218,7 @@ def update_bed(expanded_scaffold):
         #print key
         cum_len = 0
         breaks_list = []
-        for i in xrange(1,len(scaffolds_current[key]),2):
+        for i in range(1,len(scaffolds_current[key]),2):
             utg = scaffolds_current[key][i].split(':')[0]
             cum_len += unitig_length[utg]
             positions = breakpoints[key]
@@ -228,7 +228,7 @@ def update_bed(expanded_scaffold):
                     #print "found"
                     breaks_list.append(i)
                     break
-        print breaks_list
+        print(breaks_list)
         if len(breaks_list) == 0:
             scaffolds_new['scaffold_'+str(scaff_id)] = scaffolds_current[key]
             scaff_id += 1
@@ -237,8 +237,8 @@ def update_bed(expanded_scaffold):
             #print 'here'
             first_part = scaffolds_current[key][:breaks_list[0]+1]
             second_part = scaffolds_current[key][breaks_list[0]+1:]
-            print "first part : " + str(first_part)
-            print "second part : " + str(second_part)
+            print("first part : " + str(first_part))
+            print("second part : " + str(second_part))
             first_id = 'scaffold_'+str(scaff_id)
             scaff_id += 1
             second_id = 'scaffold_'+str(scaff_id)
@@ -250,23 +250,23 @@ def update_bed(expanded_scaffold):
         else:
             prev = 0
             prev_scaffold = ''
-            for i in xrange(len(breaks_list)):
+            for i in range(len(breaks_list)):
                 if i == len(breaks_list) - 1:
-                    print "start : " + str(prev)+"\tend : " + str(breaks_list[i]+1)
+                    print("start : " + str(prev)+"\tend : " + str(breaks_list[i]+1))
                     scaff = scaffolds_current[key][prev:breaks_list[i]+1]
-                    print "part : " + str(scaff)
+                    print("part : " + str(scaff))
                     scaffolds_new['scaffold_'+str(scaff_id)] = scaff
                     scaff_id += 1
-                    print "start : "+str(breaks_list[i]+1)
+                    print("start : "+str(breaks_list[i]+1))
                     scaff = scaffolds_current[key][breaks_list[i]+1:]
-                    print "part : " + str(scaff)
+                    print("part : " + str(scaff))
                     scaffolds_new['scaffold_'+str(scaff_id)] = scaff
                     avoid_file.write(prev_scaffold+'\t'+'scaffold_'+str(scaff_id)+'\n')
                     scaff_id += 1
                     continue
-                print  'start = '+str(prev)+'\tend = '+ str(breaks_list[i]+1)
+                print('start = '+str(prev)+'\tend = '+ str(breaks_list[i]+1))
                 scaff = scaffolds_current[key][prev:breaks_list[i]+1]
-                print "part : " + str(scaff)
+                print("part : " + str(scaff))
                 prev = breaks_list[i]+1
                 scaffolds_new['scaffold_'+str(scaff_id)] = scaff
                 if prev_scaffold == '':
@@ -275,9 +275,9 @@ def update_bed(expanded_scaffold):
                     avoid_file.write(prev_scaffold+'\t'+'scaffold_'+str(scaff_id)+'\n')
                     prev_scaffold = 'scaffold_'+str(scaff_id)
                 scaff_id += 1
-        print "================="
+        print("=================")
 #print scaffolds_new.keys()
-pickle.dump(scaffolds_new,open(args.directory+'/scaffolds_iteration_'+str(int(args.iteration) -1)+'.p','w'))
+pickle.dump(scaffolds_new,open(args.directory+'/scaffolds_iteration_'+str(int(args.iteration) -1)+'.p','wb'))
 update_bed(scaffolds_new)
 ofile = open(args.directory+'/misasm_'+args.iteration+'.DONE','w')
 ofile.close()
diff --git a/run_pipeline.py b/run_pipeline.py
index fc18819..96b2dc5 100755
--- a/run_pipeline.py
+++ b/run_pipeline.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python2
+#!/usr/bin/env python
 import os
 import stat
 import argparse
@@ -24,9 +24,9 @@ def NG50(lengths,sz = 0):
     genome_size = sz
     if genome_size == 0:
         genome_size = sum(lengths.values())
-    contig_lengths = sorted(lengths.values(),reverse=True)
+    contig_lengths = sorted(list(lengths.values()),reverse=True)
     lensum = 0
-    for i in xrange(len(contig_lengths)):
+    for i in range(len(contig_lengths)):
         lensum += contig_lengths[i]
         if lensum >= genome_size/2:
             return contig_lengths[i]
@@ -75,7 +75,7 @@ def main():
             p = subprocess.check_output(cmd, shell=True)
             os.chmod(args.output + "/scaffold_length_iteration_1", stat.S_IRUSR | stat.S_IWUSR | stat.S_IRGRP | stat.S_IWGRP | stat.S_IROTH)
         except subprocess.CalledProcessError as err:
-            print >> sys.stderr, str(err.output)
+            print(str(err.output), file=sys.stderr)
             sys.exit(1)
 
 
@@ -104,14 +104,14 @@ def main():
        try:
            p = subprocess.check_output(cmd,shell=True)
        except subprocess.CalledProcessError as err:
-           print >> sys.stderr,str(err.output)
+           print(str(err.output), file=sys.stderr)
 
-       cmd = 'python2 ' +bin+'/correct.py  ' + args.assembly + ' '+args.output+'/input_breaks '+args.output+'/alignment_iteration_1.bed '+args.output
+       cmd = 'python ' +bin+'/correct.py  ' + args.assembly + ' '+args.output+'/input_breaks '+args.output+'/alignment_iteration_1.bed '+args.output
        log.write(cmd)
        try:
            p = subprocess.check_output(cmd,shell=True)
        except subprocess.CalledProcessError as err:
-           print >> sys.stderr, str(err.output)
+           print(str(err.output), file=sys.stderr)
 
        os.system("mv " + args.output+"//alignment_iteration_1.tmp.bed " + args.output+"//alignment_iteration_1.bed")
        os.system("mv " + args.output+"//asm.cleaned.fasta " + args.output+"//assembly.cleaned.fasta")
@@ -124,28 +124,28 @@ def main():
     #First get RE sites
     if not fileExists(args.output+'/re_counts_iteration_'+str(iter_num)):
         try:
-            cmd = 'python2 '+bin+'/RE_sites.py -a '+args.output + '/assembly.cleaned.fasta -e '+ args.enzyme + ' > '+ args.output+'/re_counts_iteration_'+str(iter_num)
-            print cmd
+            cmd = 'python '+bin+'/RE_sites.py -a '+args.output + '/assembly.cleaned.fasta -e '+ args.enzyme + ' > '+ args.output+'/re_counts_iteration_'+str(iter_num)
+            print(cmd)
             log.write(cmd+'\n')
             p = subprocess.check_output(cmd,shell=True)
 
         except subprocess.CalledProcessError as err:
             # if os.path.isfile(args.output+'/re_counts_iteration_'+str(iter_num)):
             #   os.system(args.output+'/RE_sites_iteration_'+str(iter_num))
-            print >> sys.stderr, str(err.output)
+            print(str(err.output), file=sys.stderr)
             sys.exit(1)
 
     #Now compute normal links with old new_links code
-    print >> sys.stderr, "Starting Iteration "+ str(iter_num)
+    print("Starting Iteration "+ str(iter_num), file=sys.stderr)
     if not fileExists(args.output+'/contig_links_iteration_'+str(iter_num)):
         try:
-            cmd = 'python2 '+bin+'/make_links.py -b '+ args.output+'/alignment_iteration_1.bed' + ' -d '+ args.output +' -i '+str(iter_num) + ' -x ' + args.dup
-            print cmd
+            cmd = 'python '+bin+'/make_links.py -b '+ args.output+'/alignment_iteration_1.bed' + ' -d '+ args.output +' -i '+str(iter_num) + ' -x ' + args.dup
+            print(cmd)
             log.write(cmd+'\n')
             p = subprocess.check_output(cmd,shell=True)
 
         except subprocess.CalledProcessError as err:
-            print >> sys.stderr, str(err.output)
+            print(str(err.output), file=sys.stderr)
             if os.path.isfile(args.output+'/contig_links_iteration_'+str(iter_num)):
                 os.system('rm '+args.output+'/contig_links_iteration_'+str(iter_num))
             sys.exit(1)
@@ -153,14 +153,14 @@ def main():
     #now use Serge's code to calculate
     if not fileExists(args.output+'/contig_links_scaled_iteration_'+str(iter_num)):
         try:
-            cmd =  'python2 '+bin+'/fast_scaled_scores.py -d '+args.output+' -i '+str(iter_num)
+            cmd =  'python '+bin+'/fast_scaled_scores.py -d '+args.output+' -i '+str(iter_num)
             log.write(cmd+'\n')
-            print cmd
+            print(cmd)
             p = subprocess.check_output(cmd,shell=True)
         except subprocess.CalledProcessError as err:
             if os.path.isfile(args.output+'/contig_links_scaled_iteration_'+str(iter_num)):
                 os.system('rm '+args.output+'/contig_links_scaled_iteration_'+str(iter_num))
-            print >> sys.stderr, str(err.output)
+            print(str(err.output), file=sys.stderr)
             sys.exit(1)
 
     #Sort the links by column 5
@@ -168,12 +168,12 @@ def main():
         try:
             cmd = 'sort -k 5 -gr '+args.output+'/contig_links_scaled_iteration_'+str(iter_num)+ ' > '+ args.output+'/contig_links_scaled_sorted_iteration_'+str(iter_num)
             log.write(cmd+'\n')
-            print cmd
+            print(cmd)
             p = subprocess.check_output(cmd,shell=True)
         except subprocess.CalledProcessError as err:
             if os.path.isfile(args.output+'/contig_links_scaled_sorted_iteration_'+str(iter_num)):
                 os.system('rm '+args.output+'/contig_links_scaled_sorted_iteration_'+str(iter_num))
-            print >> sys.stderr, str(err.output)
+            print(str(err.output), file=sys.stderr)
             sys.exit(1)
 
     if args.gfa != 'abc' and not os.path.isfile(args.output+'/tmp.links'):
@@ -182,7 +182,7 @@ def main():
             log.write(cmd+'\n')
             p = subprocess.check_output(cmd,shell=True)
         except  subprocess.CalledProcessError as err:
-            print >> sys.stderr, str(err.output)
+            print(str(err.output), file=sys.stderr)
             sys.exit(1)
 
         os.system('mv ' + args.output+'/tmp.links '+args.output+'/contig_links_scaled_sorted_iteration_1')
@@ -190,46 +190,46 @@ def main():
 
     if not os.path.isfile(args.output+'/scaffolds_iteration_1.p'):
         try:
-            cmd = 'python2 '+bin+'/layout_unitigs.py -x '+args.gfa + ' -l '+args.output+'/contig_links_scaled_sorted_iteration_'+str(iter_num) +' -c ' +str(args.cutoff)+' -i 1 -d '+args.output
+            cmd = 'python '+bin+'/layout_unitigs.py -x '+args.gfa + ' -l '+args.output+'/contig_links_scaled_sorted_iteration_'+str(iter_num) +' -c ' +str(args.cutoff)+' -i 1 -d '+args.output
             log.write(cmd+'\n')
-            print cmd
+            print(cmd)
             p = subprocess.check_output(cmd,shell=True)
 
         except subprocess.CalledProcessError as err:
             if os.path.isfile(args.output+'scaffolds_iteration_1.p'):
                 os.system('rm '+args.output+'scaffolds_iteration_1.p')
-            print >> sys.stderr, str(err.output)
+            print(str(err.output), file=sys.stderr)
             sys.exit(1)
     if not fileExists(args.output+'/misasm_iteration_'+str(iter_num+1)+'.report'):
         try:
             cmd = bin+'/break_contigs -a ' + args.output+'/alignment_iteration_'+str(iter_num+1)+'.bed -b ' + args.output+'/breakpoints_iteration_'+str(iter_num+1)+'.txt -l '+ args.output+'/scaffold_length_iteration_'+str(iter_num+1) + ' -i '+str(iter_num+1)+' -s 100   > ' + args.output+'/misasm_iteration_'+str(iter_num+1)+'.report'
             p = subprocess.check_output(cmd,shell=True)
-            print cmd
+            print(cmd)
             log.write(cmd+'\n')
         except subprocess.CalledProcessError as err:
-            print  >> sys.stderr, str(err.output)
+            print(str(err.output), file=sys.stderr)
             sys.exit(1)
 
     if not fileExists(args.output+'/misasm_'+str(iter_num+1)+'.DONE'):
         try:
-            cmd = 'python2 '+bin+'/refactor_breaks.py -d ' + args.output + ' -i ' + str(iter_num+1)
+            cmd = 'python '+bin+'/refactor_breaks.py -d ' + args.output + ' -i ' + str(iter_num+1)
             p = subprocess.check_output(cmd,shell=True)
-            print cmd
+            print(cmd)
             log.write(cmd+'\n')
             #os.system('mv scaffold_length_iteration_'+str(iter_num+1)+'_tmp scaffold_length_iteration'+str(iter_num+1))
             #os.system('mv re_counts_iteration_'+str(iter_num+1)+'_tmp re_counts_iteration_'+str(iter_num+1))
             #os.system('mv alignment_iteration_'+str(iter_num+1)+'_tmp.bed alignment_iteration_'+str(iter_num+1)+'.bed')
         except subprocess.CalledProcessError as err:
-            print  >> sys.stderr, str(err.output)
+            print(str(err.output), file=sys.stderr)
             sys.exit(1)
 
     if args.prnt == 'yes':
-        cmd = 'python2 ' + bin+'/get_seq.py -a '+ args.output +'/assembly.cleaned.fasta -f ' + args.output+'/scaffolds_ITERATION_'+str(iter_num)+'.fasta -g ' + args.output+'/scaffolds_ITERATION_'+str(iter_num)+'.agp -p '+ args.output+'/scaffolds_iteration_'+str(iter_num)+'.p'
+        cmd = 'python ' + bin+'/get_seq.py -a '+ args.output +'/assembly.cleaned.fasta -f ' + args.output+'/scaffolds_ITERATION_'+str(iter_num)+'.fasta -g ' + args.output+'/scaffolds_ITERATION_'+str(iter_num)+'.agp -p '+ args.output+'/scaffolds_iteration_'+str(iter_num)+'.p'
         log.write(cmd+'\n')
         try:
             p = subprocess.check_output(cmd,shell=True)
         except subprocess.CalledProcessError as err:
-            print >> sys.stderr, str(err.output)
+            print(str(err.output), file=sys.stderr)
 
 
     iter_num += 1
@@ -240,37 +240,37 @@ def main():
             scaffold_length[attrs[0]] = int(attrs[1])
         ng50.append(NG50(scaffold_length,genome_size))
     if iter_num - 1 == int(args.iter):
-        cmd ='python2 '+bin+'/get_seq.py -a '+ args.output + '/assembly.cleaned.fasta -f ' + args.output+'/scaffolds_FINAL.fasta -g ' + args.output+'/scaffolds_FINAL.agp -p '+args.output+'/scaffolds_iteration_'+str(args.iter)+'.p'
+        cmd ='python '+bin+'/get_seq.py -a '+ args.output + '/assembly.cleaned.fasta -f ' + args.output+'/scaffolds_FINAL.fasta -g ' + args.output+'/scaffolds_FINAL.agp -p '+args.output+'/scaffolds_iteration_'+str(args.iter)+'.p'
         log.write(cmd+'\n')
         os.system(cmd)
         sys.exit(0)
     #now do iterative
     while True:
-        print >> sys.stderr, "Starting Iteration "+ str(iter_num)
+        print("Starting Iteration "+ str(iter_num), file=sys.stderr)
         if not fileExists(args.output+'/contig_links_iteration_'+str(iter_num)):
             try:
-                cmd = 'python2 '+bin+'/make_links.py -b '+ args.output+'/alignment_iteration_'+str(iter_num)+'.bed' + ' -d '+ args.output +' -i '+str(iter_num)
-                print cmd
+                cmd = 'python '+bin+'/make_links.py -b '+ args.output+'/alignment_iteration_'+str(iter_num)+'.bed' + ' -d '+ args.output +' -i '+str(iter_num)
+                print(cmd)
                 p = subprocess.check_output(cmd,shell=True)
                 log.write(cmd+'\n')
                 #os.system("rm "+args.output+'/alignment_iteration_'+str(iter_num)+'.bed')
 
             except subprocess.CalledProcessError as err:
-                print >> sys.stderr, str(err.output)
+                print(str(err.output), file=sys.stderr)
                 if os.path.isfile(args.output+'/contig_links_iteration_'+str(iter_num)):
                     os.system('rm '+args.output+'/contig_links_iteration_'+str(iter_num))
                 sys.exit(1)
 
-        print >> sys.stderr, "Starting Iteration "+ str(iter_num)
+        print("Starting Iteration "+ str(iter_num), file=sys.stderr)
         if not os.path.isfile(args.output+'/contig_links_scaled_iteration_'+str(iter_num)):
             try:
-                cmd =  'python2 '+bin+'/fast_scaled_scores.py -d '+args.output+' -i '+str(iter_num)
+                cmd =  'python '+bin+'/fast_scaled_scores.py -d '+args.output+' -i '+str(iter_num)
                 log.write(cmd+'\n')
                 p = subprocess.check_output(cmd,shell=True)
             except subprocess.CalledProcessError as err:
                 if os.path.isfile(args.output+'/contig_links_scaled_iteration_'+str(iter_num)):
                     os.system('rm '+args.output+'/contig_links_scaled_iteration_'+str(iter_num))
-                print >> sys.stderr, str(err.output)
+                print(str(err.output), file=sys.stderr)
                 sys.exit(1)
 
         if not fileExists(args.output+'/contig_links_scaled_sorted_iteration_'+str(iter_num)):
@@ -281,57 +281,57 @@ def main():
             except subprocess.CalledProcessError as err:
                 if os.path.isfile(args.output+'/new_links_scaled_sorted_iteration_'+str(iter_num)):
                     os.system('rm '+args.output+'/new_links_scaled_sorted_iteration_'+str(iter_num))
-                print >> sys.stderr, str(err.output)
+                print(str(err.output), file=sys.stderr)
                 sys.exit(1)
         #NOW check if any useful link here
         if check(args.output+'/contig_links_scaled_sorted_iteration_'+str(iter_num)):
-           print >> sys.stderr, "WARNING: Not enough Hi-C reads for scaffolding"
+           print("WARNING: Not enough Hi-C reads for scaffolding", file=sys.stderr)
 
         if not fileExists(args.output+'/scaffolds_iteration_'+str(iter_num)+'.p'):
             try:
-                cmd = 'python2 '+bin+'/layout_unitigs.py -x abc -l '+args.output+'/contig_links_scaled_sorted_iteration_'+str(iter_num) +' -c ' +str(args.cutoff)+' -i '+str(iter_num)+' -d '+args.output
-                print cmd
+                cmd = 'python '+bin+'/layout_unitigs.py -x abc -l '+args.output+'/contig_links_scaled_sorted_iteration_'+str(iter_num) +' -c ' +str(args.cutoff)+' -i '+str(iter_num)+' -d '+args.output
+                print(cmd)
                 log.write(cmd+'\n')
                 p = subprocess.check_output(cmd,shell=True)
 
             except subprocess.CalledProcessError as err:
                 if os.path.isfile(args.output+'scaffolds_iteration_'+str(iter_num)+'.p'):
                     os.system('rm '+args.output+'scaffolds_iteration_'+str(iter_num)+'.p')
-                print >> sys.stderr, str(err.output)
+                print(str(err.output), file=sys.stderr)
                 sys.exit(1)
 
 
         if not os.path.isfile(args.output+'/misasm_iteration_'+str(iter_num+1)+'.report'):
             try:
                 cmd = bin+'/break_contigs -a ' + args.output+'/alignment_iteration_'+str(iter_num+1)+'.bed -b ' + args.output+'/breakpoints_iteration_'+str(iter_num+1)+'.txt -l '+ args.output+'/scaffold_length_iteration_'+str(iter_num+1) + ' -i '+str(iter_num+1)+' -s 100  > ' + args.output+'/misasm_iteration_'+str(iter_num+1)+'.report'
-                print cmd
+                print(cmd)
                 log.write(cmd+'\n')
                 p = subprocess.check_output(cmd,shell=True)
             except subprocess.CalledProcessError as err:
-                print  >> sys.stderr, str(err.output)
+                print(str(err.output), file=sys.stderr)
                 sys.exit(1)
 
         if not os.path.isfile(args.output+'/misasm_'+str(iter_num+1)+'.DONE'):
             try:
-                cmd = 'python2 '+bin+'/refactor_breaks.py -d ' + args.output + ' -i ' + str(iter_num+1) + ' > '+args.output+'/misasm_'+str(iter_num+1)+'.log'
-                print cmd
+                cmd = 'python '+bin+'/refactor_breaks.py -d ' + args.output + ' -i ' + str(iter_num+1) + ' > '+args.output+'/misasm_'+str(iter_num+1)+'.log'
+                print(cmd)
                 log.write(cmd+'\n')
                 p = subprocess.check_output(cmd,shell=True)
                 #os.system('mv scaffold_length_iteration_'+str(iter_num+1)+'_tmp scaffold_length_iteration'+str(iter_num+1))
                 #os.system('mv re_counts_iteration_'+str(iter_num+1)+'_tmp re_counts_iteration_'+str(iter_num+1))
                 #os.system('mv alignment_iteration_'+str(iter_num+1)+'_tmp.bed alignment_iteration_'+str(iter_num+1)+'.bed')
             except subprocess.CalledProcessError as err:
-                print  >> sys.stderr, str(err.output)
+                print(str(err.output), file=sys.stderr)
                 sys.exit(1)
 
 
         if args.prnt == 'yes':
-            cmd = 'python2 ' + bin+'/get_seq.py -a '+ args.output +'/assembly.cleaned.fasta -f ' + args.output+'/scaffolds_ITERATION_'+str(iter_num)+'.fasta -g ' + args.output+'/scaffolds_ITERATION_'+str(iter_num)+'.agp -p '+ args.output+'/scaffolds_iteration_'+str(iter_num)+'.p'
+            cmd = 'python ' + bin+'/get_seq.py -a '+ args.output +'/assembly.cleaned.fasta -f ' + args.output+'/scaffolds_ITERATION_'+str(iter_num)+'.fasta -g ' + args.output+'/scaffolds_ITERATION_'+str(iter_num)+'.agp -p '+ args.output+'/scaffolds_iteration_'+str(iter_num)+'.p'
             log.write(cmd+'\n')
             try:
                 p = subprocess.check_output(cmd,shell=True)
             except subprocess.CalledProcessError as err:
-                print >> sys.stderr, str(err.output)
+                print(str(err.output), file=sys.stderr)
 
         scaffold_length = {}
         with open(args.output+'/scaffold_length_iteration_'+str(iter_num+1),'r') as f:
@@ -341,14 +341,14 @@ def main():
             ng50.append(NG50(scaffold_length,genome_size))
             curr_sz = len(ng50)
             if ng50[curr_sz - 1] == ng50[curr_sz - 2]:
-                cmd ='python2 '+bin+'/get_seq.py -a '+ args.output + '/assembly.cleaned.fasta -f ' + args.output+'/scaffolds_FINAL.fasta -g ' + args.output+'/scaffolds_FINAL.agp -p '+args.output+'/scaffolds_iteration_'+str(iter_num-1)+'.p'
+                cmd ='python '+bin+'/get_seq.py -a '+ args.output + '/assembly.cleaned.fasta -f ' + args.output+'/scaffolds_FINAL.fasta -g ' + args.output+'/scaffolds_FINAL.agp -p '+args.output+'/scaffolds_iteration_'+str(iter_num-1)+'.p'
                 log.write(cmd+'\n')
                 os.system(cmd)
                 sys.exit(0)
 
 
         if iter_num - 1 == int(args.iter):
-            cmd ='python2 '+bin+'/get_seq.py -a '+ args.output + '/assembly.cleaned.fasta -f ' + args.output+'/scaffolds_FINAL.fasta -g ' + args.output+'/scaffolds_FINAL.agp -p '+args.output+'/scaffolds_iteration_'+str(args.iter)+'.p'
+            cmd ='python '+bin+'/get_seq.py -a '+ args.output + '/assembly.cleaned.fasta -f ' + args.output+'/scaffolds_FINAL.fasta -g ' + args.output+'/scaffolds_FINAL.agp -p '+args.output+'/scaffolds_iteration_'+str(args.iter)+'.p'
             log.write(cmd+'\n')
             os.system(cmd)
             sys.exit(0)
diff --git a/stitch.py b/stitch.py
index 720ff6e..b5ef337 100755
--- a/stitch.py
+++ b/stitch.py
@@ -22,12 +22,12 @@ def parse_fasta(fh):
             fa[current_short_name] = []
         else:
             fa[current_short_name].append(ln.rstrip())
-    for short_name, nuc_list in fa.iteritems():
+    for short_name, nuc_list in fa.items():
         fa[short_name] = ''.join(nuc_list)
     return fa
 
 
-scaffolds = pickle.load(open(args.pickle,'r'))
+scaffolds = pickle.load(open(args.pickle,'rb'))
 
 contig_seqs = parse_fasta(open(args.contigs,'r'))
 unitig_seqs = parse_fasta(open(args.unitigs,'r'))
@@ -68,7 +68,7 @@ def parse_fasta(fh):
     contig_end = 0
     path_normal = []
     path_with_ori = []
-    for i in xrange(0,len(path),2):
+    for i in range(0,len(path),2):
        path_normal.append(path[i].split(':')[0])
        if path[i].split(':')[1] + path[i+1].split(':')[1] == 'BE':
         path_with_ori.append(path[i].split(':')[0]+':FOW')
@@ -166,9 +166,9 @@ def parse_fasta(fh):
 
     scaffold_seq = ''
     gap = ''
-    for i in xrange(500):
+    for i in range(500):
         gap += 'N'
-    for i in xrange(len(new_path)):
+    for i in range(len(new_path)):
         if len(new_path[i]) != 4:
             utg,ori = new_path[i].split(':')
             if ori == 'FOW':
@@ -191,14 +191,14 @@ def parse_fasta(fh):
                 scaffold_seq += gap
     ofile.write('>scaffold_'+str(scaffold_id)+'\n')
     scaffold_id += 1
-    chunks = [scaffold_seq[i:i+80] for i in xrange(0,len(scaffold_seq),80)]
+    chunks = [scaffold_seq[i:i+80] for i in range(0,len(scaffold_seq),80)]
     for each in chunks:
         ofile.write(each+'\n')
 
-    print "=============================="
-    print path_with_ori
-    print new_path
-    print "============================="
+    print("==============================")
+    print(path_with_ori)
+    print(new_path)
+    print("=============================")