2.1.0

This release adds support for misassembly correction and scaffolding
using linked reads, using Tigmint and ARCS. (Tigmint and
ARCS must be installed separately.) In addition, simultaneous optimization
of s (seed length) and n (min supporting read pairs / Chromium barcodes)
is now supported during scaffolding.

abyss-longseqdist:

• Fix hang on input SAM containing no alignments with MAPQ > 0

abyss-pe:

• New lr parameter. Provide linked reads (i.e. 10x Genomics
  Chromium reads) via this parameter to perform misassembly
  correction and scaffolding using Chromium barcode information.
  Requires Tigmint and ARCS tools to be installed in addition
  to ABySS.
• Fix bug where j (threads) was not being correctly passed to
  to bgzip/pigz
• Fix bug where zsh time/memory profiling was not being used,
  even when zsh was available

abyss-scaffold:

• Simultaneous optimization of n and s using line search
  or grid search [default]

SimpleGraph:

• add options -s and -n to filter paired-end paths by
  seed length and edge weight, respectively

2.0.3

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)

2.0.2

Summary

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

2.0.1

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).

2.0.0

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 [email protected]

• 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!)

1.9.0

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 [email protected]

• 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.

1.5.2

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 [email protected]

• 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.

1.5.1

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 [email protected]

• 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

1.5.0

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 [email protected]

• 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.

1.3.7

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 [email protected]

• 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.