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Published by benvvalk almost 6 years ago
This release improves scaffold N50 on human by ~10%, due to implementation of a new --median
option for DistanceEst
(thanks to @lcoombe!). This release also adds a new --max-cost
option for konnector
and abyss-sealer
that curbs indeterminately long running times, particularly at low k values.
abyss-pe:
DistanceEst --median
option as theDockerfile:
DistanceEst:
--median
optionkonnector:
--max-cost
option to bound running timesealer:
--max-cost
option to bound running timePublished by benvvalk about 6 years ago
This release provides bug fixes and modest improvements to
Bloom filter assembly contiguity/correctness. Parallelization
of Sealer has also been improved, thanks to contributions by
@vlad0x00.
abyss-bloom-dbg:
kc
parameter now also applies to MPI assemblies (see below)abyss-fac:
ABYSS-P:
--kc
option, with implements a hard minimum k-merabyss-pe:
zsh: no such option: pipefail
error withzsh
(fallback to bash
instead)time=1
now times all assembly commandsabyss-sealer:
--gap-file
option (thanks to @vlad0x00!)DistanceEst:
Published by benvvalk over 6 years ago
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:
abyss-pe:
lr
parameter. Provide linked reads (i.e. 10x Genomicsj
(threads) was not being correctly passed tobgzip
/pigz
zsh
time/memory profiling was not being used,zsh
was availableabyss-scaffold:
n
and s
using line searchSimpleGraph:
-s
and -n
to filter paired-end paths byPublished by benvvalk over 6 years ago
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:
abyss-pe graph=gfa2
abyss-bloom:
abyss-bloom build -t rolling-hash
option, toabyss-bloom-dbg
abyss-bloom kmers -r
abyss-bloom-dbg:
-i
option to read Bloom filter files built byabyss-bloom build -t rolling-hash
abyss-map:
ABYSS-P:
abyss-pe:
gzip
with pigz
, if availablezsh
, if availableN
instead of n
for scaffold stage,abyss-samtobreak:
--alignment-length
(-a
) option to exclude alignments--contig-length
(-l
) option to exclude contigs--genome-size
(-G
) option, for contiguity metrics--mapq
(-q
) option for minimum MAPQ score--patch-gaps
(-g
) option to join alignmentsabyss-todot:
--add-complements
optionabyss-tofastq:
--bx
option to copy BX tag from from SAM/BAMPublished by benvvalk almost 8 years ago
Fix compile errors with gcc-6 and boost-1.62.
Published by benvvalk about 8 years ago
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).
Published by benvvalk about 8 years ago
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.
2016-08-30 Ben Vandervalk [email protected]
abyss-bloom:
abyss-bloom-dbg:
abyss-fatoagp:
abyss-pe:
abyss-sealer:
konnector:
README.md:
Published by benvvalk over 9 years ago
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.
2015-05-28 Ben Vandervalk [email protected]
abyss-bloom:
-j
option forabyss-map:
--protein
option for mapping protein sequences.abyss-pe:
k
to the k-mer pair span and K
to size of analigner=dida
option for using the DIDA parallel alignmentgraph=gfa
option to use the GFA (Graphicalabyss-sealer:
konnector:
--extend
option for extending merged and unmergedPublished by traymond over 10 years ago
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.
2014-07-09 Anthony Raymond [email protected]
ABYSS:
abyss-bloom:
abyss-fixmate:
unordered_map::quick_erase
.abyss-longseqdist:
error: invalid CIGAR
when reading BWA output.configure:
konnector:
Published by traymond over 10 years ago
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.
2014-05-07 Anthony Raymond [email protected]
abyss-filtergraph --assemble --SS
.abyss-filtergraph:
--assemble --SS
abyss-pe:
ABYSS-P:
Published by traymond over 10 years ago
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.
2014-01-15 Anthony Raymond [email protected]
abyss-pe:
Q
, to mask low quality bases to N.xtip=1
, to remove 2-in 0-out tips.ss=1
, to perform strand-specific assemblyscaftigs
. Breaks scaffold sequences at 'N's andlong
parameterabyss-fixmate:
DistanceEst:
abyss-fixmate:
ABYSS/ABYSS-P:
abyss-layout:
abyss-map:
abyss-overlap:
abyss-PathOverlap:
abyss-scaffold:
AdjList:
Overlap:
PopBubbles:
Published by traymond almost 11 years ago
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.
2013-11-20 Anthony Raymond [email protected]
abyss-fac:
abyss-filtergraph:
abyss-map:
abyss-longseqdist:
abyss-mergepairs:
abyss-overlap:
abyss-pe:
ABYSS-P:
abyss-samtobreak:
UnitTest:
Published by traymond about 11 years ago
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.