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ChangeLog
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2024-09-11 Johnathan Wong <[email protected]>
* Release version 2.3.9
General:
* Deallocate memory used by alignment data structure in dialign
2024-07-18 Lauren Coombe <[email protected]>
* Release version 2.3.8
General:
* Type changes to allow building with LTO
2023-05-16 Lauren Coombe <[email protected]>
* Release version 2.3.7
General:
* Fix build on macOS-12 and macOS-13 (Thanks @parham-k!)
2023-05-02 Lauren Coombe <[email protected]>
* Release version 2.3.6
General:
* btllib is now a dependency
* Documentation updates
abyss-rresolver-short:
* btllib source code removed due to btllib now being a dependency
2022-05-11 Vladimir Nikolic <[email protected]>
* Release version 2.3.5
General:
* Fixed compile errors when using the -DNDEBUG flag.
* Removed deprecated C++ features.
2021-12-20 Vladimir Nikolic <[email protected]>
* Release version 2.3.4
General:
* Dropped support for gcc5 due to lack of support for more recent C++ features.
abyss-rresolver-short:
* Reduced memory consumption.
* Better calculation of read size proportions in the input dataset.
* Increased max read read size allowed.
2021-11-10 Vladimir Nikolic <[email protected]>
* Release version 2.3.3
General:
* Fixed a contig overlap distance assertion.
abyss-rresolver-short:
* Multiple read sizes are better handled. E.g. 150 and 151 are processed as one read size.
* Updated default parameters.
2021-10-13 Vladimir Nikolic <[email protected]>
* Release version 2.3.2
General:
* Updated the `m` parameter and the `S` and `N` scaffolding parameters to better defaults.
abyss-rresolver-short:
* Updated btllib to 1.1.7
2021-04-21 Vladimir Nikolic <[email protected]>
* Release version 2.3.1
abyss-rresolver-short:
* Fixed a bug that crashed ABySS if Bloom filter size is not specified.
* Fixed a compilation error for clang-10.
2021-03-22 Vladimir Nikolic <[email protected]>
* Release version 2.3.0
General:
* The RResolver algorithm is now part of the default pipeline. RResolver resolves repeats using short reads and generates assemblies with better contiguity and often fewer misassemblies.
2020-09-17 Johnathan Wong <[email protected]>
* Release version 2.2.5
General:
* Resolve various compilation errors in newer versions of clang
* Use ntHash's 0th hash as the default hash instead of the 1st hash
* Added optional RResolver module, not currently part of the ABySS assembly pipeline
abyss-rresolver-short:
* Improves genome assemblies at unitig stage by using a sliding window at read size level
across repeats to determine which paths are correct
* For further information: consult http://www.birollab.ca/assets/posts/195_Nikolic_Vladimir_HiTSeq_ISMB2020.pdf
misc:
* Extract all tags in a SAM file
2020-01-30 Johnathan Wong <[email protected]>
* Release version 2.2.4
General:
* Refactor deprecated functions in clang-8
Sealer:
* Remove unsupported -D option from help page
abyss-bloom:
* Add counting Bloom Filter instruction to help page
abyss-bloom-dbg:
* Report coverage information of unitigs
2019-09-20 Johnathan Wong <[email protected]>
* Release version 2.2.3
* Revert memory consumption of Bloom filters to pre 2.2.0 behaviour
ABySS will now share the specified memory among all Bloom filters
instead of just the counting Bloom filter.
* Fix gcc-9 compilation warnings
2019-08-16 Johnathan Wong <[email protected]>
* Release version 2.2.2
* Fix abyss-overlap for 32-bit systems
2019-08-12 Johnathan Wong <[email protected]>
* Release version 2.2.1
* Fix abyss-bloom for macOS
2019-08-01 Johnathan Wong <[email protected]>
* Release version 2.2.0
* Construct a counting Bloom filter instead of a cascading Bloom filter.
abyss-bloom:
* Add 'counting' as valid argument to '-t' option to build a counting
bloom filter
2018-12-04 Sauparna Palchowdhury <[email protected]>
* Release version 2.1.5
* Compiler fixes and increse stack size limits to avoid stack overflows.
abyss-pe:
* Add 'ulimit' statements to the Makefile to increse a thread's
stack size to 64MB.
2018-11-09 Ben Vandervalk <[email protected]>
* Release version 2.1.4
* Major improvements to Bloom filter assembly contiguity and
correctness. Bloom filter assemblies now have equivalent scaffold
contiguity and better correctness than MPI assemblies of the same
data, while still requiring less than 1/10th of the memory. On
human, Bloom filter assembly times are still a few hours longer
than MPI assemblies (e.g. 17 hours vs. 13 hours, using 48
threads).
abyss-pe:
* Change default value of `m` from 50 => 0, which has the effect
of disallowing sequence overlaps < k-1 bp. QUAST tests on E. coli /
C. elegans / H. sapiens showed that both contiguity and
correctness were improved by allowing only overlaps of k-1 bp
between sequence ends.
2018-11-05 Ben Vandervalk <[email protected]>
* Release version 2.1.3
* Bug fix release
abyss-bloom:
* Added `graph` command for visualizing neighbourhoods of the
Bloom filter de Bruijn graph (produces GraphViz)
abyss-fixmate-ssq:
* Fixed missing tab in SAM output which broke ABySS linked reads
pipeline (Tigmint/ARCS)
2018-10-24 Ben Vandervalk <[email protected]>
* Release version 2.1.2
* Improved scaffold N50 on human by ~10% by
implementing a new `DistanceEst --median`
option (thanks to @lcoombe!)
* Added a `--max-cost` option to `konnector` and
`abyss-sealer`. This address a long-standing issue
with indeterminately long running times, particularly
for low values of `k`.
abyss-pe:
* Use the new `DistanceEst --median` option as the
default for the scaffolding stage
Dockerfile:
* Fix OpenMPI setup
DistanceEst:
* Added `--median` option
konnector:
* Added `--max-cost` option to bound running time
sealer:
* Added `--max-cost` option to bound running time
2018-09-11 Ben Vandervalk <[email protected]>
* Release version 2.1.1
abyss-bloom-dbg:
* upgrade to most recent version of ntHash to reduce
some assembly/hashing artifacts. On a human assembly, this
reduced QUAST major misassemblies by 5% and increased
scaffold contiguity by 10%
* `kc` parameter now also applies to MPI assemblies (see below)
abyss-fac:
* change N20 and N80 to N25 and N75, respectively
ABYSS-P:
* add `--kc` option, with implements a hard minimum k-mer
multiplicity cutoff
abyss-pe:
* fix `zsh: no such option: pipefail` error with
old versions of `zsh` (fallback to `bash` instead)
* adding `time=1` now times *all* assembly commands
abyss-sealer:
* parallelize gap sealing with OpenMP (thanks to
@vlad0x00!)
* add `--gap-file` option (thanks to @vlad0x00!)
DistanceEst:
* add support for GFA output
2018-04-13 Ben Vandervalk <[email protected]>
* Release version 2.1.0
* Adds support for misassembly correction and scaffolding
using linked reads, using Tigmint and ARCS. (Tigmint and
ARCS must be installed separately.)
* Support simultaneous optimization of `s` (min sequence length)
and `n` (min supporting read pairs / Chromium barcodes)
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
2018-03-14 Ben Vandervalk <[email protected]>
* Release version 2.0.3
* 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)
2016-10-21 Ben Vandervalk <[email protected]>
* Release version 2.0.2
* Fix compile errors with gcc 6 and boost 1.62
2016-09-14 Ben Vandervalk <[email protected]>
* Release version 2.0.1
* Resolve licensing issues by switching to standard GPL-3 license
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:
* Fixes to documentation of ABYSS and abyss-pe parameters
(thanks to @nsoranzo!)
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.
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.
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
2014-05-01 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.
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.
2013-07-15 Anthony Raymond <[email protected]>
* Release version 1.3.6
* Improved documentation for GitHub devs.
* ABYSS-P performance improvement.
* Various portability and bug fixes.
abyss-mergepairs:
* Fix program name.
abyss-fac:
* New option --exp-size to give the expected genome size needed
for NG50 calculation.
* New option --count-ambig include ambiguities in calculations.
ABYSS/ABYSS-P:
* Performance improvement. Runtime reduced by ~20%.
* Fix support for MPICH.
abyss-map:
* No longer require POPCNT instruction.
* New option --order to force output order the same as input.
abyss-filtergraph:
* New option --remove to remove specified contigs from graph.
PopBubbles:
* Bug fix. Setting branches > 2 will now work.
abyss-fixmate:
* Improved error when first and second read IDs do not match.
* New option --cov to compute and store the physical coverage in
a Wiggle file.
AdjIO:
* Bug fix for non-GCC compilers.
2013-03-04 Anthony Raymond <[email protected]>
* Release version 1.3.5
* Standardized --help message format.
* Improve documentation.
* Merge overlapping read pairs.
* Layout and merge contigs using sequence overlap graph.
* Attempt to fill scaffold gap with consensus of all paths between
contigs.
abyss-pe:
* Attempt to fill scaffold gap with consensus of all paths between
contigs.
AdjList:
* Increase the default value of m from 30 to 50.
abyss-overlap:
* Increase the default value of m from 30 to 50.
* New options, --tred and --no-tred. Remove transitive edges.
Default --tred.
abyss-mergepairs:
* New program. Merges overlapping read pairs.
ABYSS-P:
* Bug fix. Exit when there is a problem reading a file.
* Don't store sequences in the rank 0 process when using at least
1000 cores. Improves memory distribution with large number of
cores.
abyss-fac:
* Increase the default value of t from 200 to 500.
DistanceEst:
* Bug fix. Exit with success if there is only one contig. Fixes
this error:
DistanceEst: DistanceEst.cpp:534: int main(int, char**): Assertion `in' failed.
* Bug fix. Fix the bug causing this error:
DistanceEst: error: The observed fragment of size 128 bp is shorter than 2*l (l=71). Decrease l to 64.
* Bug fix. Correctly estimate distance using MLE when l=0.
abyss-layout:
* New program. Layout contigs using the sequence overlap graph.
abyss-map:
* Return helpful error when query ID starts with '@`
* New options, --chastity and --no-chastity. Ignore chastity
failed reads. Default --no-chastity.
abyss-samtobreak:
* New script. Calculate contig and scaffold contiguity and
correctness metrics.
abyss-fixmate:
* New option, l. Minimum alignment length. Set unmapped flag if
the CIGAR match length is too small.
* Print all alignments when the histogram output file not given.
* Print SAM header to the same file when given.
2012-05-30 Shaun Jackman <[email protected]>
* Release version 1.3.4.
* Do not extend paths, which can cause misassemblies.
* Increase the default value of m from 30 to 50.
* Various portability fixes.
abyss-pe:
* Increase the default value of m from 30 to 50 to reduce the
likelihood of misassemblies.
* Integrate with SLURM. Thanks to Timothy Carlson.
ABYSS:
* Use CityHash64 rather than Bob Jenkins' hashlittle.
SimpleGraph:
* Do not extend paths. Closes #8. Extending paths can cause
misassemblies when the de Bruijn graph is incomplete.
MergePaths:
* Bug fix. Closes #6. Fix the bug causing the error:
Assertion `!m_ambig' failed.
abyss-fatoagp:
* New script. Create a FASTA file of scaftigs and an AGP file.
2012-03-13 Shaun Jackman <[email protected]>
* Release version 1.3.3.
* New parameter, l. Specify the minimum alignment length when
aligning the reads to the contigs.
* Improve the scaffolding algorithm that identifies repeats.
* Improve the documentation.
abyss-pe:
* New parameter, l. Specify the minimum alignment length when
aligning the reads to the contigs. This option may be specified
per library. The default value is k.
* New parameter, S. Specify the minimum contig size required for
building scaffolds.
* New parameter, N. Specify the minimum number of pairs required
for building scaffolds.
* Integrate with Load Sharing Facility (LSF).
* Calculate the assembly contiguity statistics.
KAligner, abyss-map:
* Rename the minimum alignment length option -k to -l.
DistanceEst:
* Dual licensed under the GPL and BCCA-Academic licenses.
* New options, --fr and --rf. Specify the orientation of the
library. The default behaviour is to detect the orientation.
* New options, --mind and --maxd. Specify the minimum and maximum
distances for the maximum likelihood estimator.
* New option, -l, --min-align. Specify the minimum alignment
length of the aligner, which can improve distance estimates.
* Increase the default minimum mapping quality, -q, to 10, was 1.
MergePaths:
* Bug fix. Fix the bug causing the error:
Assertion `count(it2+1, path2.end(), pivot) == 0' failed.
PathConsensus:
* Bug fix. Fix the bug causing the error:
Assertion `fstSol.size() == sndSol.size()' failed.
MergeContigs:
* Calculate the assembly contiguity statistics.
abyss-scaffold:
* Improve the algorithm that identifies repeats.
* Remove simple cycles from the scaffold graph.
* Calculate the assembly contiguity statistics.
* The option -s may specify a range, such as -s200-10000,
to find the value of s that maximizes the scaffold N50.
abyss-fac:
* New option, -m, --mmd. Output MultiMarkdown format.
abyss-index:
* New option, -a, --alphabet. Specify the alphabet.
* New option, --bwt. Output the Burrows-Wheeler transform.
abyss-samtoafg:
* New script. Convert a SAM file to an AMOS AFG file.
README, README.html, abyss-pe.1:
* Improve the documentation.
2011-12-13 Shaun Jackman <[email protected]>
* Release version 1.3.2.
* Enable scaffolding by default.
* Remove small shim contigs.
* Improved distance estimates.
* Reduce sequence duplication.
* Read compressed files on Mac OS X.
abyss-pe:
* Enable scaffolding by default. If the mp parameter is not
specified, use a default value of ${pe} or ${lib}.
* Support using bowtie2 to align reads to contigs by specifying
aligner=bowtie2.
* The default aligner is abyss-map.
* Output the scaffold overlap graph, ${name}-scaffolds.dot.
* Set DYLD_FORCE_FLAT_NAMESPACE to read compressed files on OS X.
ABYSS:
* Can read k-mer count data from a Jellyfish file with extension
.jf for k-mer counts or .jfq for q-mer counts. Jellyfish must be
installed.
* Bug fix. Fix the bug causing the error
bool chomp(std::string&, char): Assertion `s.length() > 1' failed.
abyss-filtergraph:
* New program. Remove small shim contigs that add no useful
sequence to the assembly. Thanks to Tony Raymond (tgr).
PopBubbles:
* New option, -a, --branches. Specify the maximum number of
branches of a bubble that may be popped. Default is 2.
* Use DIALIGN-TX for multiple sequence alignment. Thanks to tgr.
DistanceEst:
* Improved distance estimates.
abyss-joindist:
* Remove this program. Use abyss-todot instead.
MergePaths:
* Use a non-greedy algorithm that reduces sequence duplication but
may reduce contiguity. The greedy algorithm may be used by
specifying the option --greedy.
abyss-fixmate:
* Do not output query names by default.
configure:
* New option, --enable-samseqqual. Enable SAM sequence and quality
fields.
2011-10-24 Shaun Jackman <[email protected]>
* Release version 1.3.1.
* Read sequence files in SRA format. The tool fastq-dump from the
sratoolkit must be installed.
* Read a contig overlap graph in the ASQG format of SGA.
* Fix compile errors for Mac OS X.
* Fix the bug that caused the line number of an error in a FASTQ
file to be reported incorrectly.
abyss-pe:
* Support using BWA-SW to align reads to contigs by specifying
aligner=bwasw.
* The parameter ALIGNER_OPTIONS may be used to specify a different
value for k when aligning using abyss-map.
* New target, bam, may be used to produce a final BAM file of the
reads aligned to the scaffolds.
KAligner:
* Fix the bug causing the error:
Assertion `qstep >= 0 && qstep <= m_hashSize' failed.
abyss-scaffold:
* The result is independent of the order in which the mate-pair
libraries are specified.
* Permit scaffolding contigs that have non-numeric identifiers.
* The overlap graph is optional.
abyss-todot:
* Convert adj, dist or ASQG formatted graph files to dot format.
* Merge multiple graph files into one.
2011-09-09 Shaun Jackman <[email protected]>
* Release version 1.3.0.
* Use mate-pair libraries to scaffold contigs.
* Support CASAVA-formatted FASTQ files.
* Bug fix. Do not trim quality 41 bases from the ends of reads.
* Boost C++ Libraries are required to compile ABySS.
abyss-pe:
* New parameter, mp, to specify the mate-pair libraries to be used
for scaffolding.
* Increase the default value for s from 100 to 200.
* Set the default value for n to 10.
* Integrate with PBS.
abyss-scaffold:
* New program. Scaffold using mate-pair libraries.
DistanceEst:
* Ignore multimapped alignments with a mapping quality of zero.
* New option, -q, --min-mapq. Ignore alignments with mapping
quality less than this threshold. Default is 1.
* Do not use OpenMP 3.0.
PopBubbles:
* Scaffold over complex bubbles with the option --scaffold.
Disabled by default.
MergePaths:
* Fix a bug that causes PathOverlap to die with the error:
Distance get(edge_bundle_t, const Graph&, ContigNode, ContigNode):
Assertion `e.second' failed.
* New option, --no-greedy. Use a non-greedy algorithm that reduces
sequence duplication but reduces contiguity. Disabled by default.
KAligner:
* Performance improvements. Thanks to Tony Raymond (tgr).
* The output is printed in the same order as the input when
multithreaded. (tgr)
abyss-map:
* New program. Use the BWT and FM-index to find the longest common
substring. To use it, specify the option aligner=map to abyss-pe.
abyss-index:
* New program. Build a FM-index of a FASTA file.
abyss-bowtie:
* Use abyss-tofastq --interleave to speed up abyss-fixmate.
abyss-bwa:
* Use bwa index -a bwtsw by default.
* Use abyss-tofastq --interleave to speed up abyss-fixmate.
abyss-fac:
* Report N80, N50 and N20. Do not report median and mean.
* Increase the default minimum contig size threshold, option -t,
from 100 to 200.
abyss-fixmate:
* Set the mapping quality of both alignments to the minimum
mapping quality of the pair of alignments.
abyss-tofastq:
* New option, -i, --interleave. Interleave the files.
configure:
* New option, --with-boost. Specify the path for Boost.
* New option, --disable-popcnt. Do not use the popcnt instruction.
2011-04-15 Shaun Jackman <[email protected]>
* Release version 1.2.7.
abyss-pe:
* Support using bwa or bowtie to align reads to contigs.
Specify aligner=bwa or aligner=bowtie.
* Integrate with IBM LoadLeveler.
PopBubbles:
* Use an affine gap penalty.
* The default maximum bubble length is 10 kbp.
* New option, --scaffold. Scaffold over bubbles with insufficient
sequence identity to be popped.
SimpleGraph:
* New parameter d to specify the acceptable error of a distance
estimate. The default is 6 bp.
PathConsensus:
* Use an affine gap penalty.
MergePaths:
* Fix a bug that causes PathOverlap to die with the error:
Distance get(edge_bundle_t, const Graph&, ContigNode, ContigNode):
Assertion `e.second' failed.
2011-02-07 Shaun Jackman <[email protected]>
* Release version 1.2.6.
* Find contigs that overlap by fewer than k-1 bp.
* Pop bubbles with sufficient sequence identity.
* Merge paths that overlap unambiguously.
abyss-pe:
* New parameter, m, the minimum number of overlapping bases.
The default is 30.
* The minimum sequence identity parameter, p, applies to both
PopBubbles and PathConsensus.
ABYSS:
* Support values of k larger than 96. The maximum value of k is
set when compiling using `configure --enable-maxk´.
AdjList:
* Find sequences that overlap by fewer than k-1 bp. The parameter
m specifies the minimum number of overlapping bases.
PopBubbles:
* Align both branches of the bubble and pop bubbles whose sequence
identity is sufficient, at least 90% by default.
* New parameter, p, the minimum identity required.
* The maximum bubble size is unlimited by default. This limit can
be changed using the parameter b.
SimpleGraph:
* Extend each path as long as is unambiguously possible.
PathOverlap:
* Merge paths that overlap unambiguously.