1.5.2
Summary
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.
ChangeLog
2014-07-09 Anthony Raymond traymond@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.