Release 2.0.3 · bcgsc/abyss (original) (raw)

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)