[Samtools-devel] Goby 2.0 released

[Fabien C. <fa...@me...>]

Dear all,

We are pleased to announce that Goby 2.0 <http://goby.campagnelab.org/> has
been released and integrated in the latest release of IGV (2.1.20). Version
2 is a major milestone for the Goby project which brings state of the art
alignment compression, robust SAM/BAM import exports, a parallel large sort
implementation and more. See the new tutorial ‘What’s new in Goby
2.0‘<http://campagnelab.org/software/goby/tutorials/whats-new-in-goby-2-0/>
 for detailed information.

We created a feature comparison
matrix<http://campagnelab.org/software/goby/feature-matrix/>that
contrasts
Goby 1.x, 2.0, BAM, CRAM and FASTQ.  Regarding compression, our benchmarks
indicate that Goby 2.0 can compress various datasets substantially better
than CRAM, while retaining perfect data fidelity, at speeds comparable to
the processing of BAM files.

Please note that Goby provides two file formats. One format is designed to
store reads (extension .compact-reads) and the other format to store
alignments (basename.entries, basename.header, basename.index). With two
file formats, we can always store reads in the order the sequencing
facility generated them. This avoids subtle problems some groups have
noticed when one stores reads in BAM format sorted in genomic order (see
earlier post by Richard Durbin on this thread, 'randomised read sort order
for bwa searching from BAM'). These problems are non-issues when storing
reads and alignments with Goby.

Finally, starting with Goby 2.0, we will be hosting the project source code
on GitHub <https://github.com/CampagneLaboratory/goby>, to facilitate
source code discussions and contributions from the community. Also new is a
public forum to discuss the project, request new features, ask questions
about existing tools, at
https://groups.google.com/forum/?fro...goby-framework<https://groups.google.com/forum/?fromgroups#!forum/goby-framework>

As usual, we look forward to critical feedback from the SAM/BAM community.
Thanks to everybody for previous feedback on Goby 1.

http://goby.campagnelab.org


Fabien Campagne, PhD -- http://campagnelab.org

Assistant Professor,    Dept. of Physiology and Biophysics
                         Institute for Computational Biomedicine
Associate Director,      Biomedical Informatics Core,
                      Clinical Translational Science Center

Weill Medical College of Cornell University
phone:  (646)-962-5613  1305 York Avenue
fax:    (646)-962-0383  Box 140
New York, NY 10021

See how GobyWeb can help simplify your NGS projects at
http://gobyweb.campagnelab.org