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Old 04-29-2011, 05:21 AM   #1
Fabien Campagne
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Location: New York City

Join Date: Feb 2010
Posts: 39
Default Goby 1.9.5 released, BWA, GSNAP, IGV2 support, VCF format, genotype calling and more

We have released Goby 1.9.5. Goby is a framework and tool box for efficient next-gen analysis (RNA-Seq, sequence variations including genotypes, allelic expression or estimation of methylation rates). The frameworks is compatible with Java, Python C and C++. The 1.9.5 release includes several new features.

Goby is now supported natively in BWA, GSNAP or IGV 2 early release version.

New features bring support for the Variant Call Format. The mode discover-sequence-variants outputs VCF files. This mode supports a choice of
sequence variation analyses, including:
- support to call genotypes (not appropriate for low coverage, but flies for 20x+ and very high coverage),
- estimate methylation rates in bisulfite treated reads or
- perform allelic frequency tests across groups of samples (see this new tutorial).

We also have completely reviewed and edited the web site to make sure documentation is up to date with all the changes. Importantly, the installation instructions have been rewritten form scratch and cross-references have been added to help locate relevant information.

Last, but not least, we have reduced memory usage for loading large alignments (>100M reads) and improved performance quite a bit. See the change log for more information about Goby 1.9.5 or download it here. For more details about this release, see our detailed change log.

Last edited by Fabien Campagne; 04-29-2011 at 05:38 AM. Reason: more descriptive thread title
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