[Inchworm-users] New inchworm release (02-21-2011)
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bhaas
From: Brian J H. <bh...@br...> - 2011-02-21 17:24:55
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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 -- -- Brian J. Haas Manager, Bioinformatics Outreach, Genome Annotation and Analysis The Broad Institute http://broad.mit.edu/~bhaas |