tweed

A database to store and analyze the results of oases de novo assembly pipeline. Inspired by oases2csv. The database is built by parsing the following files from the standard oases output:

• stats.txt
• contig-ordering.txt
• transcripts.fa

The resulting transcripts are annotated with coverage information calculated as geometric mean of the nodes comprising the tranascript and grouped by loci.

The best transcript in the locus is selected as the transcript in top 20% by length having the maximum coverage.

If transcripts.fa is blasted against a genome of interest, the resulting .xml output file can be imported to annotate transcripts that produced blast hits.

Dependencies

• django
• django-pagination
• gunicorn
• scipy
• monoseq
• biopython
• matplotlib

TODO

• views: by assembly, by locus, best transcript in locus
• blast annotations for transcripts
• tunable length cutoff for the best in locus transcript selection