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ChangeLog
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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
@schutzekatze!)
* add `--gap-file` option (thanks to @schutzekatze!)
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.
MergeContigs:
* Perform an alignment of the two sequences when no simple overlap
is found.
abyss-fac:
* New option, -g. Specify the expected genome size.
2010-11-15 Shaun Jackman <[email protected]>
* Release version 1.2.5.
AdjList:
* Fix the colour-space-specific bug causing the error
Assertion `seq.length() > (unsigned)opt::overlap' failed.
PathConsensus:
* Fix the bug causing the error
Assertion `fstSol.size() == 1' failed.
abyss-fixmate:
* Do not output the @RG header record at the end of the output
that gives the median fragment size. It breaks `samtools view -S`.
* --no-qname: New option. Set the qname to *.
2010-10-13 Shaun Jackman <[email protected]>
* Release version 1.2.4.
ABYSS-P:
* Fix the bug causing the error
Unexpected sequence extension message.
KAligner:
* Reduce the amount of memory used by KAligner.
PathConsensus:
* New program. Replace gaps of Ns that span a region of ambiguous
sequence with a consensus sequence of the possible sequences that
fill the gap. By default a minimum 90% identity is required. This
default can be changed with the parameter, p. The consensus
sequence uses IUPAC-IUB ambiguity codes. DIALIGN-TX is used for
the multiple sequence alignment.
PathOverlap:
* Fix the bug causing the error
Assertion `back(paths, u) == front(paths, v)' failed.
2010-09-08 Shaun Jackman <[email protected]>
* Release version 1.2.3.
ABYSS-P:
* Bug fix. Fix the bug causing the error
Assertion `m_comm.receiveEmpty()' failed.
PopBubbles:
* Bug fix. Fix the bug causing the error
error: unexpected ID
PathOverlap:
* Include the single-end contigs in the overlap graph.
abyss-pe:
* Output an overlap graph of the paired-end assembly in the file
${name}-contigs.dot.
* Do not create the intermediate file ${name}-4.fa.
abyss-adjtodot:
* Convert an overlap graph in adj format to Graphviz dot format or
SAM alignment format.
2010-08-25 Shaun Jackman <[email protected]>
* Release version 1.2.2.
* Merge contigs after popping bubbles.
* Handle multi-line FASTA sequences.
* Report the amount of memory used.
* Most tools can output their results in SAM format, including
AdjList, KAligner, ParseAligns and PathOverlap.
abyss-pe:
* New command, se-dot. Output a Graphviz dot file of the
single-end assembly.
ABYSS:
* Handle multi-line FASTA sequences.
* Report the amount of memory used.
* Improve error messages for incorrectly-formatted FASTA files.
* Bug fix. Improved handling of palindromes.
PopBubbles:
* Merge contigs after popping bubbles.
* Bug fix. Do not pop bubbles resulting from palindromes.
KAligner:
* Report the amount of memory used.
* New option, --sam. Output the alignments in SAM format.
ParseAligns, DistanceEst:
* Bug fix. The CIGAR string was oriented with respect to the
query rather than with respect to the target, which is standard.
AdjList, PathOverlap:
* New option, --sam. Output the adjacency graph in SAM format.
abyss-fixmate:
* New program. Similar to samtools fixmate, but does not require
that the input be sorted by query ID, although it is faster if it
is sorted.
2010-07-12 Shaun Jackman <[email protected]>
* Release version 1.2.1.
* Handle reverse-forward oriented mate pair libraries.
* Improved distance estimates, particularly with large fragment
libraries.
abyss-pe:
* New commands:
se-contigs: Assemble single-end contigs.
pe-contigs: Assemble paired-end contigs (default).
se-sam: Output a gzipped SAM file of the single-end assembly.
se-bam: Ouptut a BAM file of the single-end assembly.
pe-dot: Output a Graphviz dot file of the paired-end assembly.
all: Sam as se-bam pe-contigs pe-dot.
* Options for one particular library may be specified:
lib='lib1 lib2' lib2_s=1000 lib2_n=25
* Input sequence may come from an arbitrary command, which is
useful to assemble a region of an aligned BAM file:
in='<(samtools view genome.bam chr10)'
ABYSS:
* Bug fix. When reading SAM/BAM files, the quality format
incorrectly defaulted to ASCII-64, when it should be ASCII-33.
ABYSS-P:
* May use the Intel MPI library.
ParseAligns:
* Count the number of forward-reverse, reverse-forward and
forward-forward oriented alignments.
DistanceEst:
* Handle reverse-forward oriented mate pair libraries.
* Improved distance estimates, particularly with large fragment
libraries.
* Remove duplicate mate pairs.
* Print a pretty UTF-8 bar plot of the fragment-size distribution.
* Multithreaded using OpenMP. The -j, --threads option specifies
the number of threads to use.
* Performance improvment.
Overlap:
* Handle cases when more than one gap occurs within the mate pair
fragment size.
SimpleGraph:
* Performance improvment.
MergePaths:
* Handle the case when a circular sequence is assmembled into a
single contig.
abyss-tofastq:
* New program. Convert qseq, export, SAM and BAM files to FASTA or
FASTQ format. The files may be compressed with gz, bz2 or xz and
may be tarred.
2010-05-25 Shaun Jackman <[email protected]>
* Release version 1.2.0.
* Scaffold over gaps in coverage and unresolved repetitive
sequence using Ns.
* Read sequence from SAM and BAM files.
abyss-pe:
* Set q=3 by default. Trim bases from the ends of reads whose
quality is less than 3.
* Do not store the .pair.gz file.
* Generate a BAM file of the mate pairs that align to
different contigs of the single-end assembly. Disabled by default.
* Output a Graphviz dot file of the paired-end assembly.
Disabled by default.
* Store the bubbles in ${name}-bubbles.fa rather than bubbles.fa.
* Store the indel bubbles in ${name}-indel.fa.
* Bug fix for mawk.
ABYSS:
* Set -E0 when coverage is low (<2).
ABYSS-P:
* Remove the temporary files contigs-*.fa and snp-*.fa.
PopBubbles:
* Output in Graphviz dot format using --dot.
KAligner:
* Do not ignore sequences (reads or contigs) containing N.
* Output SAM headers (but not SAM alignments).
ParseAligns:
* Output in SAM format.
DistanceEst:
* Input in SAM format.
* Output in Graphviz dot format using --dot.
Overlap:
* Scaffold over gaps in coverage. Scaffolding can be disabled
using the option --no-scaffold.
* Merge contigs that overlap at simple repeats. These merges can
be prevented using the option --no-merge-repeat.
SimpleGraph:
* Scaffold over repeats. Scaffolding can be disabled using the
option --no-scaffold.