[Inchworm-users] new Inchworm, and initial Trinity release

[Brian J H. <bh...@br...>]

Greetings all.

Two important messages:

1.  A new version of Inchworm is now available:
http://sourceforge.net/projects/inchworm/files/inchworm-03132011.tgz/download

It includes contributions from Michael Ott and Alexie Papanicolao that (a)
leverage OpenMP for parallel multi-core faster parsing of inputed read
sequences, and (b) faster bit-level reverse complementing of sequences for
faster processing in double-stranded RNA-Seq assembly mode.

2.  Our initial release of Trinity is now available at
http://TrinityRNASeq.sf.net

Trinity uses Inchworm followed by two additional new tools: Chrysalis and
Butterfly, which provide for full-length reconstruction of alternatively
spliced isoforms and improved assembly of transcripts derived from
paralogous genes.   Code, documentation, and sample data are available from
the Trinity website.  The Trinity download includes the most recent version
of Inchworm.

We'll continue to maintain both sites, since there are additional
Inchworm-based applications that haven't been migrated over to Trinity just
yet, such as genome-guided de novo transcript assembly and integration with
PASA for genome annotation.

Best wishes,

-Brian


-- 
-- 
Brian J. Haas
Manager, Bioinformatics Outreach, Genome Annotation and Analysis
The Broad Institute
http://broad.mit.edu/~bhaas