seqkit v2.7.0

Author: shenwei356

commands.csv

@@ -1,39 +1,39 @@
-category,command,function,input,strand-sensitivity,multi-threads,popularity
-basic,[seq](https://bioinf.shenwei.me/seqkit/usage/#seq),"transform sequences: extract ID/seq, filter by length/quality, remove gaps…",FASTA/Q,,,★★★★★
-,[stats](https://bioinf.shenwei.me/seqkit/usage/#stats),"simple statistics: #seqs, min/max_len, N50, Q20%, Q30%…",FASTA/Q,,✓,★★★★★
-,[subseq](https://bioinf.shenwei.me/seqkit/usage/#subseq),"get subsequences by region/gtf/bed, including flanking sequences",FASTA/Q,+ or/and -,,★★★
-,[sliding](https://bioinf.shenwei.me/seqkit/usage/#sliding),extract subsequences in sliding windows,FASTA/Q,+ only,,★★
-,[faidx](https://bioinf.shenwei.me/seqkit/usage/#faidx),create FASTA index file and extract subsequence (with more features than samtools faidx),FASTA,+ or/and -,,
-,[watch ](https://bioinf.shenwei.me/seqkit/usage/#watch ),monitoring and online histograms of sequence features,FASTA/Q,,,
-,[sana](https://bioinf.shenwei.me/seqkit/usage/#sana),sanitize broken single line FASTQ files,FASTQ,,,
-,[scat ](https://bioinf.shenwei.me/seqkit/usage/#scat ),real time concatenation and streaming of fastx files,FASTA/Q,,✓,
-format conversion,[fq2fa](https://bioinf.shenwei.me/seqkit/usage/#fq2fa),convert FASTQ to FASTA,FASTQ,,,★★
-,[fx2tab](https://bioinf.shenwei.me/seqkit/usage/#fx2tab),convert FASTA/Q to tabular format,FASTA/Q,,,★★
-,[fa2fq](https://bioinf.shenwei.me/seqkit/usage/#fa2fq),retrieve corresponding FASTQ records by a FASTA file,FASTA/Q,+ only,,
-,[tab2fx](https://bioinf.shenwei.me/seqkit/usage/#tab2fx),convert tabular format to FASTA/Q format,FASTA/Q,,,
-,[convert](https://bioinf.shenwei.me/seqkit/usage/#convert),"convert FASTQ quality encoding between Sanger, Solexa and Illumina",FASTA/Q,,,
-,[translate](https://bioinf.shenwei.me/seqkit/usage/#translate),translate DNA/RNA to protein sequence,FASTA/Q,+ or/and -,,★★
-searching,[grep](https://bioinf.shenwei.me/seqkit/usage/#grep),"search sequences by ID/name/sequence/sequence motifs, mismatch allowed",FASTA/Q,+ and -,"partly, -m",★★★★★
-,[locate](https://bioinf.shenwei.me/seqkit/usage/#locate),"locate subsequences/motifs, mismatch allowed",FASTA/Q,+ and -,"partly, -m",★★★★★
-,[amplicon](https://bioinf.shenwei.me/seqkit/usage/#amplicon),"extract amplicon (or specific region around it), mismatch allowed",FASTA/Q,+ and -,"partly, -m",★
-,[fish](https://bioinf.shenwei.me/seqkit/usage/#fish),look for short sequences in larger sequences,FASTA/Q,+ and -,,
-set operation,[sample](https://bioinf.shenwei.me/seqkit/usage/#sample),sample sequences by number or proportion,FASTA/Q,,,★★★★
-,[rmdup](https://bioinf.shenwei.me/seqkit/usage/#rmdup),remove duplicated sequences by ID/name/sequence,FASTA/Q,+ and -,,★★★
-,[common](https://bioinf.shenwei.me/seqkit/usage/#common),find common sequences of multiple files by id/name/sequence,FASTA/Q,+ and -,,
-,[duplicate](https://bioinf.shenwei.me/seqkit/usage/#duplicate),duplicate sequences N times,FASTA/Q,,,★
-,[split](https://bioinf.shenwei.me/seqkit/usage/#split),split sequences into files by id/seq region/size/parts (mainly for FASTA),FASTA preffered,,,★
-,[split2](https://bioinf.shenwei.me/seqkit/usage/#split2),"split sequences into files by size/parts (FASTA, PE/SE FASTQ)",FASTA/Q,,,★★
-,[head](https://bioinf.shenwei.me/seqkit/usage/#head),print first N FASTA/Q records,FASTA/Q,,,
-,[head-genome](https://bioinf.shenwei.me/seqkit/usage/#head-genome),print sequences of the first genome with common prefixes in name,FASTA/Q,,,
-,[range](https://bioinf.shenwei.me/seqkit/usage/#range),print FASTA/Q records in a range (start:end),FASTA/Q,,,
-,[pair](https://bioinf.shenwei.me/seqkit/usage/#pair),match up paired-end reads from two fastq files,FASTA/Q,,,
-edit,[concat](https://bioinf.shenwei.me/seqkit/usage/#concat),concatenate sequences with same ID from multiple files,FASTA/Q,+ only,,★★★
-,[replace](https://bioinf.shenwei.me/seqkit/usage/#replace),replace name/sequence by regular expression,FASTA/Q,+ only,,★★
-,[restart](https://bioinf.shenwei.me/seqkit/usage/#restart),reset start position for circular genome,FASTA/Q,+ only,,★
-,[mutate](https://bioinf.shenwei.me/seqkit/usage/#mutate),"edit sequence (point mutation, insertion, deletion)",FASTA/Q,+ only,,
-,[rename](https://bioinf.shenwei.me/seqkit/usage/#rename),rename duplicated IDs,FASTA/Q,,,★
-ordering,[sort](https://bioinf.shenwei.me/seqkit/usage/#sort),sort sequences by id/name/sequence/length,FASTA preffered,,,★★
-,[shuffle](https://bioinf.shenwei.me/seqkit/usage/#shuffle),shuffle sequences,FASTA preffered,,,
-BAM processing,[bam](https://bioinf.shenwei.me/seqkit/usage/#bam),monitoring and online histograms of BAM record features,BAM,,,
-others,[sum](https://bioinf.shenwei.me/seqkit/usage/#sum),compute message digest for all sequences in FASTA/Q files,FASTA/Q,,✓,
-,[merge-slides](https://bioinf.shenwei.me/seqkit/usage/#merge-slides),merge sliding windows generated from seqkit sliding,text,,,
+Category,Command,Function,Input,Strand-sensitivity,Multi-threads
+Basic operation,[seq](https://bioinf.shenwei.me/seqkit/usage/#seq),"Transform sequences: extract ID/seq, filter by length/quality, remove gaps…",FASTA/Q,,
+,[stats](https://bioinf.shenwei.me/seqkit/usage/#stats),"Simple statistics: #seqs, min/max_len, N50, Q20%, Q30%…",FASTA/Q,,✓
+,[subseq](https://bioinf.shenwei.me/seqkit/usage/#subseq),"Get subsequences by region/gtf/bed, including flanking sequences",FASTA/Q,+ or/and -,
+,[sliding](https://bioinf.shenwei.me/seqkit/usage/#sliding),Extract subsequences in sliding windows,FASTA/Q,+ only,
+,[faidx](https://bioinf.shenwei.me/seqkit/usage/#faidx),Create the FASTA index file and extract subsequences (with more features than samtools faidx),FASTA,+ or/and -,
+,[translate](https://bioinf.shenwei.me/seqkit/usage/#translate),translate DNA/RNA to protein sequence,FASTA/Q,+ or/and -,
+,[watch ](https://bioinf.shenwei.me/seqkit/usage/#watch ),Monitoring and online histograms of sequence features,FASTA/Q,,
+,[scat ](https://bioinf.shenwei.me/seqkit/usage/#scat ),Real time concatenation and streaming of fastx files,FASTA/Q,,✓
+Format conversion,[fq2fa](https://bioinf.shenwei.me/seqkit/usage/#fq2fa),Convert FASTQ to FASTA format,FASTQ,,
+,[fx2tab](https://bioinf.shenwei.me/seqkit/usage/#fx2tab),Convert FASTA/Q to tabular format,FASTA/Q,,
+,[fa2fq](https://bioinf.shenwei.me/seqkit/usage/#fa2fq),Retrieve corresponding FASTQ records by a FASTA file,FASTA/Q,+ only,
+,[tab2fx](https://bioinf.shenwei.me/seqkit/usage/#tab2fx),Convert tabular format to FASTA/Q format,TSV,,
+,[convert](https://bioinf.shenwei.me/seqkit/usage/#convert),"Convert FASTQ quality encoding between Sanger, Solexa and Illumina",FASTA/Q,,
+Searching,[grep](https://bioinf.shenwei.me/seqkit/usage/#grep),"Search sequences by ID/name/sequence/sequence motifs, mismatch allowed",FASTA/Q,+ and -,"partly, -m"
+,[locate](https://bioinf.shenwei.me/seqkit/usage/#locate),"Locate subsequences/motifs, mismatch allowed",FASTA/Q,+ and -,"partly, -m"
+,[amplicon](https://bioinf.shenwei.me/seqkit/usage/#amplicon),"Extract amplicon (or specific region around it), mismatch allowed",FASTA/Q,+ and -,"partly, -m"
+,[fish](https://bioinf.shenwei.me/seqkit/usage/#fish),Look for short sequences in larger sequences,FASTA/Q,+ and -,
+Set operation,[sample](https://bioinf.shenwei.me/seqkit/usage/#sample),Sample sequences by number or proportion,FASTA/Q,,
+,[rmdup](https://bioinf.shenwei.me/seqkit/usage/#rmdup),Remove duplicated sequences by ID/name/sequence,FASTA/Q,+ and -,
+,[common](https://bioinf.shenwei.me/seqkit/usage/#common),Find common sequences of multiple files by id/name/sequence,FASTA/Q,+ and -,
+,[duplicate](https://bioinf.shenwei.me/seqkit/usage/#duplicate),Duplicate sequences N times,FASTA/Q,,
+,[split](https://bioinf.shenwei.me/seqkit/usage/#split),Split sequences into files by id/seq region/size/parts (mainly for FASTA),FASTA preffered,,
+,[split2](https://bioinf.shenwei.me/seqkit/usage/#split2),"Split sequences into files by size/parts (FASTA, PE/SE FASTQ)",FASTA/Q,,
+,[head](https://bioinf.shenwei.me/seqkit/usage/#head),Print first N FASTA/Q records,FASTA/Q,,
+,[head-genome](https://bioinf.shenwei.me/seqkit/usage/#head-genome),Print sequences of the first genome with common prefixes in name,FASTA/Q,,
+,[range](https://bioinf.shenwei.me/seqkit/usage/#range),Print FASTA/Q records in a range (start:end),FASTA/Q,,
+,[pair](https://bioinf.shenwei.me/seqkit/usage/#pair),Patch up paired-end reads from two fastq files,FASTA/Q,,
+Edit,[replace](https://bioinf.shenwei.me/seqkit/usage/#replace),Replace name/sequence by regular expression,FASTA/Q,+ only,
+,[rename](https://bioinf.shenwei.me/seqkit/usage/#rename),Rename duplicated IDs,FASTA/Q,,
+,[concat](https://bioinf.shenwei.me/seqkit/usage/#concat),Concatenate sequences with same ID from multiple files,FASTA/Q,+ only,
+,[restart](https://bioinf.shenwei.me/seqkit/usage/#restart),Reset start position for circular genome,FASTA/Q,+ only,
+,[mutate](https://bioinf.shenwei.me/seqkit/usage/#mutate),"Edit sequence (point mutation, insertion, deletion)",FASTA/Q,+ only,
+,[sana](https://bioinf.shenwei.me/seqkit/usage/#sana),Sanitize broken single line FASTQ files,FASTQ,,
+Ordering,[sort](https://bioinf.shenwei.me/seqkit/usage/#sort),Sort sequences by id/name/sequence/length,FASTA preffered,,
+,[shuffle](https://bioinf.shenwei.me/seqkit/usage/#shuffle),Shuffle sequences,FASTA preffered,,
+BAM processing,[bam](https://bioinf.shenwei.me/seqkit/usage/#bam),Monitoring and online histograms of BAM record features,BAM,,
+Miscellaneous,[sum](https://bioinf.shenwei.me/seqkit/usage/#sum),Compute message digest for all sequences in FASTA/Q files,FASTA/Q,,✓
+,[merge-slides](https://bioinf.shenwei.me/seqkit/usage/#merge-slides),Merge sliding windows generated from seqkit sliding,TSV,,