ABySS 1.9.0 (May 29, 2015)


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 Disptached Alignment) parallel alignment framework.

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

Available downloads

Source code

For Linux (1 MB)

Change log

2015-05-28 Ben Vandervalk <benv@bcgsc.ca>

* Release version 1.9.0
* New paired de Bruijn graph mode for assembly.
* First official release of Sealer, a tool for closing
scaffold gaps by navigating a Bloom filter de Bruijn graph.
* New outward extension feature for Konnector to generate long pseudo-reads.
* Support for the DIDA (Distributed Indexing Dispatched Alignment) framework, for computing sequence alignments in parallel across multiple machines.
* Unit tests can now be run easily with 'make check', without external dependencies.

* abyss-bloom 'build' command now supports -j option for multi-threaded Bloom filter construction.

* New --protein option for mapping protein sequences.

* New paired de Bruijn graph mode for assembly. Enable by setting `k` to the k-mer pair span and `K` to size of an individual k-mer in a k-mer pair. See README.md for further details.
* New `aligner=dida` option for using the DIDA parallel alignment framework. See the DIDA section of the abyss-pe man page for usage details.
* New `graph=gfa` option to use the GFA (Graphical Fragment Assembly) format for intermediate graph files.

* New tool for closing scaffold gaps by navigating a Bloom filter de Bruijn graph
* See Sealer/README.md or abyss-sealer man page for details and examples.

* New --extend option for extending merged and unmerged reads outwards in the de Bruijn graph.