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danbing-tk v1.3

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@joyeuxnoel8 joyeuxnoel8 released this 25 Jun 18:42
· 203 commits to master since this release
v1.3
689c2f7
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Learn about vigilant mode.

Improvements:

  • Significantly improve the time/mem usage of danbing-tk
    • benchmark setting
      • 31x HG00731 SRS sample from 1000 Genomes Project
      • two-consortium RPGG, 81045 loci
      • 16 cores xeon-2665, avx
      • samtools fasta -@2 -n $bam | danbing-tk -a -kf 4 1 -gc 80 -k 21 -qs pan -fa /dev/stdin -o $out -p 16 -cth 45 | gzip >$aln
    • Sample was genotyped in ~43 min using 31.4 Gb mem
    • 24x speedup, 37% reduction in mem usage
    • Output file size: 1.3 Gb
  • danbing-tk now takes binary graph/index as input
    • ktools serialze was added to convert *kmers to *.graph.umap *.kmerDBi.umap and *.kmerDBi.vv
  • bam2pe is now merged with danbing-tk
    • use -fa option for non-interleaved fasta e.g. samtools fasta -@2 -n $bam
    • use -fai for interleaved fasta

Resources

  • New RPGG and VNTR coordinates on 35 HGSVC genomes are available at Zenodo
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