2.0.2

@benvvalk benvvalk released this Oct 21, 2016 · 5 commits to master since this release

Summary

Fix compile errors with gcc-6 and boost-1.62.

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2.0.1

@benvvalk benvvalk released this Sep 14, 2016 · 15 commits to master since this release

Summary

This release resolves some licensing issues with that were pointed out in 2.0.0. As of 2.0.1, ABySS is now available under a standard GPL-3 license, and the libraries included under lib/rolling-hash and lib/bloomfilter are now also licensed under GPL-3. For alternative licensing terms, please contact Patrick Rebstein (prebstein at bccancer.bc.ca).

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2.0.0

@benvvalk benvvalk released this Sep 1, 2016 · 21 commits to master since this release

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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1.9.0

@benvvalk benvvalk released this May 29, 2015 · 223 commits to master since this release

Summary

This release introduces a new paired de Bruijn graph mode for assembly. In paired de Bruijn graph mode, ordinary k-mers are replaced by k-mer pairs, where each k-mer pair is separated by a fixed-size gap. The primary advantage of paired de Bruijn graph mode is that the span of a k-mer pair can be arbitrarily wide without consuming additional memory, and thus provides improved scalability for assemblies of long sequencing reads.

This release also introduces a new tool called Sealer for closing scaffold gaps, new Konnector functionality for producing long pseudo-reads, and support for the DIDA (Distributed Indexing Dispatched Alignment) parallel alignment framework.

ChangeLog

2015-05-28 Ben Vandervalk benv@bcgsc.ca

  • Release version 1.9.0
  • New paired de Bruijn graph mode for assembly.
  • First official release of Sealer, a tool for closing
    scaffold gaps by navigating a Bloom filter de Bruijn graph.
  • New outward extension feature for Konnector to generate
    long pseudo-reads.
  • Support for the DIDA (Distributed Indexing Dispatched
    Alignment) framework, for computing sequence alignments
    in parallel across multiple machines.
  • Unit tests can now be run easily with 'make check', without
    external dependencies.

abyss-bloom:

  • abyss-bloom 'build' command now supports -j option for
    multi-threaded Bloom filter construction.

abyss-map:

  • New --protein option for mapping protein sequences.

abyss-pe:

  • New paired de Bruijn graph mode for assembly. Enable by
    setting k to the k-mer pair span and K to size of an
    individual k-mer in a k-mer pair. See README.md for further
    details.
  • New aligner=dida option for using the DIDA parallel alignment
    framework. See the DIDA section of the abyss-pe man page
    for usage details.
  • New graph=gfa option to use the GFA (Graphical
    Fragment Assembly) format for intermediate graph files.

abyss-sealer:

  • New tool for closing scaffold gaps by navigating a Bloom
    filter de Bruijn graph
  • See Sealer/README.md or abyss-sealer man page for details
    and examples.

konnector:

  • New --extend option for extending merged and unmerged
    reads outwards in the de Bruijn graph.

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1.5.2

@traymond traymond released this Jul 9, 2014 · 720 commits to master since this release

Summary

In this release we introduce Konnector, a fast and memory-efficient tool to fill the gap between paired-end reads. Konnector determines the intervening sequence by building a Bloom filter de Bruijn graph and searching for paths between paired-end reads within the graph. A companion tool called abyss-bloom is also provided which can be used to construct reusable bloom filter files for input to Konnector; otherwise, Konnector will build an in-memory Bloom filter for one-time use. In addition to Konnector, we have fixed bugs related to compiling with GCC 4.8+ and parsing BWA output SAM files.

ChangeLog

2014-07-09 Anthony Raymond traymond@bcgsc.ca

  • Release version 1.5.2
  • First official release of Konnector and abyss-bloom.
  • More GCC 4.8+ fixes! Modified Boost install instructions.
  • Fixed rare bug when parsing output of BWA.

ABYSS:

  • New option, --mask-cov, use kmers with lowercased bases, but
    don't count them towards multiplicity.

abyss-bloom:

  • Construct reusable Bloom filter files for use with Konnector.
  • Perform boolean operations on two or more bloom filters.
    Currently supports union and intersection operations.

abyss-fixmate:

  • Check for boost 1.43+ when using unordered_map::quick_erase.
  • New option, --all, to report all alignments.
  • Set mate unmapped flag for mateless reads.

abyss-longseqdist:

  • Fixed error: invalid CIGAR when reading BWA output.

configure:

  • Include mpi and boost libraries as system libraries. Silences
    warnings (treated as errors) when compiling with GCC 4.8+.

konnector:

  • Merge read pairs into a single sequence (pseudoread) by
    building a Bloom filter de Bruijn graph and searching for paths
    between the paired end reads. Input reads may be
    FASTA/FASTQ/SAM/BAM. The input files must be sorted by read name
    and may not contain orphan reads.

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1.5.1

@traymond traymond released this May 8, 2014 · 883 commits to master since this release

Summary

In this release we fix a compatibility issue with Trans-ABySS 1.5.0 where the output of abyss-filtergraph is not strand-specific. Also, we include a FCC portability fix.

ChangeLog

2014-05-07 Anthony Raymond traymond@bcgsc.ca

  • Release version 1.5.1
  • Fix an issue with strand-specific RNA-Seq assembly when running
    abyss-filtergraph --assemble --SS.
  • Portability fixes for Fujitsu C Compiler (FCC).

abyss-filtergraph:

  • Assemble contigs in forward orientation with --assemble --SS

abyss-pe:

  • Fix some cases where abyss-pe uses incorrect executables

ABYSS-P:

  • Portability fix with FCC

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1.5.0

@traymond traymond released this May 1, 2014 · 888 commits to master since this release

Summary

In this release we have added full strand specific RNA-Seq support such that output contigs are correctly oriented with respect to the original transcripts sequenced. Also, there are new parameters to abyss-pe, xtip and Q, that are used to improve assembly in high coverage regions like highly expressed transcripts. Setting xtip=1 will more aggressively remove certain tips. The Q parameter will prevent low quality bases from being used in the assembly. The version has been bumped to 1.5.0 to signify compatibility with Trans-ABySS 1.5.0.

ChangeLog

2014-01-15 Anthony Raymond traymond@bcgsc.ca

  • Release version 1.5.0
  • Assemble strand-specific RNA-Seq libraries into strand-specific
    contigs.
  • New parameters, Q and xtip. Improves assembly in high-coverage
    regions by removing recurrent read errors.
  • Portability fixes for Fujitsu C Compiler.

abyss-pe:

  • New parameter, Q, to mask low quality bases to N.
  • New parameter, xtip=1, to remove 2-in 0-out tips.
  • New parameter, ss=1, to perform strand-specific assembly
    using ssRNA-Seq libraries.
  • New command, scaftigs. Breaks scaffold sequences at 'N's and
    produce a scaftigs.fa file.
  • Include long-scaffs.fa in FAC statistics if long parameter
    used.

abyss-fixmate:

  • Performance improvement for GCC-4.6 and older.

DistanceEst:

  • Report an estimation of duplicate fragments from read pairs
    mapping to different contigs.

abyss-fixmate:

  • Report number of fragments removed as noise and outliers.

ABYSS/ABYSS-P:

  • New option, --SS, to support strand-specific assembly.

abyss-layout:

  • New option, --SS, to support strand-specific assembly.

abyss-map:

  • New option, --SS, to support strand-specific assembly.

abyss-overlap:

  • New option, --SS, to support strand-specific assembly.

abyss-PathOverlap:

  • New option, --SS, to support strand-specific assembly.

abyss-scaffold:

  • New option, --SS, to support strand-specific assembly.
  • Don't prune xtips when scaffolding.

AdjList:

  • New option, --SS, to support strand-specific assembly.

Overlap:

  • New option, --SS, to support strand-specific assembly.

PopBubbles:

  • New option, --SS, to support strand-specific assembly.

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1.3.7

@traymond traymond released this Dec 11, 2013 · 964 commits to master since this release

Summary

Scaffolds can now be rescaffolded using long sequences such as RNA-Seq assemblies produced from Trans-ABySS. Added support for gcc 4.8+ and Mac OS X 10.9 Mavericks with clang. Finally, we've licensed ABySS under GPL for non-commercial purposes. Please read the LICENSE file for more details.

ChangeLog

2013-11-20 Anthony Raymond traymond@bcgsc.ca

  • Release version 1.3.7
  • Use long sequences to rescaffold scaffolds. May be run by
    adding libraries to the `long’ parameter. When Scaffolding
    with RNA-Seq contigs from a Trans-ABySS assembly, the genic
    contiguity is greatly improved.
  • Added support gcc 4.8+, and Mac OS X 10.9 Mavericks with clang.
  • Licensed as GPL for non-commercial purposes.

abyss-fac:

  • Added e-size to contiguity statistics as described in the GAGE
    paper.

abyss-filtergraph:

  • Bug fix. `--assemble’ will not fail an assertion.
  • New option, --max-length, used to remove contigs over the
    specified threshold.
  • Trim 2-in 0-out tips when removing tips.

abyss-map:

  • Bug fix. Correctly set mapq=0 for reads that multi map.

abyss-longseqdist:

  • New program. Generate distance estimates between all contigs a
    single read maps to.

abyss-mergepairs:

  • Report number of reads chastity filtered.

abyss-overlap:

  • Bug fix. Handle ambiguity codes.

abyss-pe:

  • Support BWA-MEM with assembly. Run using parameter
    `aligner=bwamem’.
  • Added another scaffolding stage using long sequences. May be
    run by adding libraries to the `long’ parameter.

ABYSS-P:

  • Bug fix. Do not use awk to merge fasta files.

abyss-samtobreak:

  • Building bug fix. Check that ghc modules are installed.

UnitTest:

  • The Google C++ testing framework has been added to ABySS.

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