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.

Release version 1.3.6

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.

1.0.11

• Release version 1.0.11.
• Assemble colour-space reads. Read identifiers must be named with
  the suffixes F3 and R3.
• Read files in qseq format. Thanks to Tony Raymond (tgr).
• Prevent misassemblies mediated by tandem segmental duplications.
  A sequence XRRY, where R is a repeat sequence, could have been
  misassembled as XRY. (tgr)

abyss-pe:

• Integrate with Sun Grid Engine (SGE). A parallel, paired-end
  assembly can be run with a single qsub command. The parameters
  lib, np and k default to the qsub environment variables JOB_NAME
  (qsub -N), NSLOTS (qsub -pe) and SGE_TASK_ID (qsub -t)
  respectively.
• The .pair file, the largest intermediate file, is now gzipped.

ABYSS-P:

• Bug fix. At k=19, k-mer would be distributed to even-numbered
  processes only.

KAligner:

• Multithreaded. The -j, --threads option specifies the number of
  threads to use. The order in which the alignments are output will
  vary from run to run, but the alignments are deterministic and
  will not vary. Each thread reads and aligns one file, so the reads
  must be in more than one file to use this feature. (tgr)