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@benvvalk benvvalk released this 14 Mar 22:25
· 439 commits to master since this release
2.0.3
cfde2ec

This minor release provides bug fixes and improved reliability for both MPI assemblies and Bloom filter assemblies on large datasets. In addition, many usability improvements have been made to the abyss-samtobreak program for misasssembly assessment.

overall:

  • Many compiler fixes for GCC >= 6, Boost >= 1.64
  • Read and write GFA 2 assembly graphs with abyss-pe graph=gfa2
  • Support reading CRAM via samtools

abyss-bloom:

  • New abyss-bloom build -t rolling-hash option, to
    pre-build input Bloom filters for abyss-bloom-dbg
  • Fix incorrect output of abyss-bloom kmers -r
    (thanks to @notestaff!)

abyss-bloom-dbg:

  • New -i option to read Bloom filter files built by
    abyss-bloom build -t rolling-hash
  • Improved error branch trimming (reduces number of
    small output sequences)
  • Fix intermittent segfaults caused by non-null-terminated
    strings

abyss-map:

  • Append BX tag to SAM output (Chromium 10x Genomics data)

ABYSS-P:

  • Increase default number of sparsehash buckets from
    200,000,000 => 1,000,000,000
  • Benefit: Allows larger datasets to be assembled without
    time-consuming sparsehash resize operations (e.g. H. sapiens)
  • Caveat: Increases minimum memory requirement per
    CPU core from 89 MB to 358 MB

abyss-pe:

  • Parallelize gzip with pigz, if available
  • Report time/memory for each program with zsh, if available
  • Fix: use N instead of n for scaffold stage,
    when set by user

abyss-samtobreak:

  • New --alignment-length (-a) option to exclude alignments
    shorter than a given length
  • New --contig-length (-l) option to exclude contigs
    shorter than a given length
  • New --genome-size (-G) option, for contiguity metrics
    that depend on the reference genome size
  • New --mapq (-q) option for minimum MAPQ score
  • New --patch-gaps (-g) option to join alignments
    separated by small gaps
  • New TSV output format with additional contiguity
    stats (e.g. L50, NG50)
  • Fix handling of hard-clipped alignments

abyss-todot:

  • New --add-complements option

abyss-tofastq:

  • New --bx option to copy BX tag from from SAM/BAM
    to FASTQ header comment (Chromium 10x Genomics
    data)
Assets 3
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