IMSA+A is an extension of Arron-IMSA program for metagenomic taxonomic classificiation using RNAseq reads.

IMSA+A should be installed into it's own directory, independent of IMSA. See Detailed Directions.

Starting with DEC 2016 update, IMSA code is distributed with IMSA+A. Very minor updates for compatability are included; said changes are documented with comments.

https://www.ncbi.nlm.nih.gov/news/03-02-2016-phase-out-of-GI-numbers/ GI numbers are being phased out (09/2106). IMSA and IMSA+A counting scripts count using GI numbers. Any files downloaded here together will function, but updated NCBI databases after 09/2016 will not. The hand off to accession.version should be relatively painless and require very minor code changes. However, IMSA+A will need NCBI to release an accession.version database dump in the same way that they do a GI dump. Until then, IMSA+A is not future compatible.

A new script "postprocesscount4acc.py" allows use of accession number data. New options in systemSettings.py, start with "ACC_" to point to a new accession version to taxon database.

We found a bug in IMSA paired end processing. We are working to correct and will release soon.