ABySS 1.5.2 is released

[Tony Raymond]

Hi everyone,

I have just released ABySS 1.5.2!

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.

Download the new release here:

http://www.bcgsc.ca/platform/bioinfo/software/abyss

Or clone/fork our Github repository:

https://github.com/bcgsc/abyss

Happy assembling!

Tony

2014-07-09 Anthony Raymond tray...@bcgsc.ca

• 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.