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24 Open 39 Closed
24 Open 39 Closed
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Issues list

Attach SV calling to Snakemake?
#64 opened Nov 5, 2024 by adamnovak
@xchang1
Add multiple minimap2 presets (lr:hq and tech-named one)
#63 opened Nov 5, 2024 by adamnovak
@adamnovak
1
Add haplotype sampling to Snakemake
#62 opened Nov 5, 2024 by adamnovak
Add a target to make the One True List of Files to the Snakemake, along with experiment configs for it
#61 opened Nov 5, 2024 by adamnovak
@xchang1
Evaluate DV calling on HG001 AKA NA12878 using its new assembly-based benchmark
#60 opened Nov 5, 2024 by adamnovak
@adamnovak
Summary Statistics Table
#59 opened Nov 5, 2024 by adamnovak
Investigate low SV calling accuracy on the unfiltered graph
#58 opened Nov 5, 2024 by adamnovak
@jmonlong
Fix very high false negative rate for insertion SVs with LRG
#55 opened Oct 23, 2024 by adamnovak
@xchang1
1
Collect speed results, sim accuracy results, and real calling results for Giraffe all together
#54 opened Sep 13, 2024 by adamnovak
Stop tracking provenance specifically when measuring speed
#52 opened Aug 6, 2024 by adamnovak
Investigate if graph alignments of nanopore reads that get long softclips at surjection are correct
#51 opened Jul 19, 2024 by adamnovak
2
Upgrade to HPRC Year1-3 data and Release 2 graphs
#50 opened Jul 11, 2024 by adamnovak
@adamnovak
Fix CHM13 HiFi reads that minimap2 gets right and Giraffe gets wrong
#47 opened Jul 8, 2024 by adamnovak
Improve MAPQs on HiFi reads
#46 opened Jul 3, 2024 by adamnovak
1
Fix HiFi reads that mismap due to increased exploration of chains
#39 opened Jun 27, 2024 by adamnovak
Work out why Banded Global Aligner middles are slow on Illumina reads
#35 opened May 24, 2024 by adamnovak
Work out why the fragment stage is slow on Illumina reads
#34 opened May 24, 2024 by adamnovak
performance of vg inject
#32 opened May 23, 2024 by netwon123
Do variant calling on lr-giraffe Illumina reads and evaluate it
#26 opened May 22, 2024 by adamnovak
Port paired end logic for sr code path
#21 opened May 16, 2024 by benedictpaten
Produce summary performance plots for R10 and Hifi
#19 opened May 16, 2024 by adamnovak
@xchang1
Long read support for vg surject
#13 opened May 6, 2024 by adamnovak
@jeizenga
Debug haplotype sampling with long read Giraffe
#12 opened May 6, 2024 by adamnovak
@jltsiren
2
Long Read Giraffe Release
#6 opened May 6, 2024 by adamnovak
2 tasks done
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