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@benvvalk benvvalk released this 01 Sep 17:49
· 584 commits to master since this release
2.0.0
92ffd21

Summary

This release introduces a new Bloom filter assembly mode that enables large genome assemblies with minimal memory (e.g. 34 GB for H. sapiens with 76X coverage bfc-corrected reads). Bloom filter assemblies are currently less contiguous than the default (MPI) assembly mode but are still of high quality (e.g. 3.5 Mbp vs. 4.8 Mbp scaffold NG50 for H. sapiens). Bloom filter assembly mode is enabled by adding three 'abyss-pe' parameters (B = Bloom filter size, H = number of Bloom filter hash functions, kc = k-mer coverage threshold). See 'README.md' for an example.

This release also updates several 'abyss-pe' parameter defaults to be more suitable for large genome assemblies with recent Illumina data. In addition, ABySS 2.0.0 includes minor usability improvements for 'abyss-sealer' and removes an unnecessary build dependency on sqlite3.

ChangeLog

2016-08-30 Ben Vandervalk benv@bcgsc.ca

  • Release version 2.0.0
  • New Bloom filter mode for assembly => assemble large genomes
    with minimal memory (e.g. 34G for H. sapiens)
  • Update param defaults for modern Illumina data
  • Make sqlite3 an optional dependency

abyss-bloom:

  • New 'compare' command for bitwise comparison of Bloom filters
    (thanks to @bschiffthaler!)
  • New 'kmers' command for printing k-mers that match a Bloom filter
    (thanks to @bschiffthaler!)

abyss-bloom-dbg:

  • New preunitig assembler that uses Bloom filter
  • Add 'B' param (Bloom filter size) to 'abyss-pe' command to enable
    Bloom filter mode
  • See README.md and '--help' for further instructions

abyss-fatoagp:

  • Mask scaftigs shorter than 50bp with 'N's (short scaftigs
    were causing problems with NCBI submission)

abyss-pe:

  • Update default parameter values for modern Illumina data
  • Change 'l=k' => 'l=40'
  • Change 's=200' => 's=1000'
  • Change 'S=s' => 'S=1000-10000' (do a param sweep of 'S')
  • Use 'DistanceEst --mean' for scaffolding stage, instead of
    the default '--mle'

abyss-sealer:

  • New '--max-gap-length' ('-G') option to replace unintuitive
    '--max-frag'; use of '--max-frag' is now deprecated
  • Require user to explicitly specify Bloom filter size (e.g.
    '-b40G')
  • Report false positive rate (FPR) when building/loading Bloom
    filters
  • Don't require input FASTQ files when using pre-built Bloom
    filter files

konnector:

  • Fix bug causing output read 2 file to be empty
  • New percent sequence identity options ('-x' and '-X')
  • New '--alt-paths-mode' option to output alternate connecting
    paths between read pairs

README.md:

  • Fix documentation of ABYSS and abyss-pe parameters
    (thanks to @nsoranzo!)
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