ABySS 1.5.2 (Jul 10, 2014)


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.

For additional information about this project, please visit the overview page .

Available downloads


For all platforms (790 kB)

Change log

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.

* New option, --mask-cov, use kmers with lowercased bases, but
don't count them towards multiplicity.

* Construct reusable Bloom filter files for use with Konnector.
* Perform boolean operations on two or more bloom filters.
Currently supports union and intersection operations.

* 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.

* Fixed `error: invalid CIGAR` when reading BWA output.

* Include mpi and boost libraries as system libraries. Silences
warnings (treated as errors) when compiling with GCC 4.8+.

* 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.