Greetings all.
A new version of Inchworm is now available here:
http://sourceforge.net/projects/inchworm/files/inchworm_r02-21-2011.tgz/download
It includes the following changes:
-cannot seed contigs from palindromic kmers
-in double-stranded mode, the reverse-complement kmers are disabled during
path extension (prevents artifactual 'fold-back' contigs resulting from
inverted-repeat-containing or palindrome-containing sequences).
-by default, prunes likely error-containing kmers, defined as candidate
extension-kmers that have an abundance less than 5% of a dominant kmer
extension. Much cleaner contig sets result, mitigating what we had called
'echo' contigs that were output based on error-containing kmers from highly
expressed transcripts. Command-line options are available to manipulate this
or turn it off altogether.
Finally, note that the full Trinity RNA-Seq assembly suite (
http://trinityrnaseq.sf.net) should be available within the next week.
Inchworm is leveraged as the front-end process in the Trinity suite, and
future Inchworm updates will be provided as part of the larger Trinity
package. Stay tuned for details.
Best regards,
-Brian
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Brian J. Haas
Manager, Bioinformatics Outreach, Genome Annotation and Analysis
The Broad Institute
http://broad.mit.edu/~bhaas
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