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@benvvalk benvvalk released this 29 May 22:38
· 786 commits to master since this release
1.9.0
0762983

Summary

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 Dispatched Alignment) parallel alignment framework.

ChangeLog

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:

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

abyss-map:

  • New --protein option for mapping protein sequences.

abyss-pe:

  • 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.

abyss-sealer:

  • 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.

konnector:

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