Rockhopper
Bacterial RNA-seq analysis: align reads to coding sequences, rRNAs, tRNAs, and miscellaneous RNAs
It can align on both the sense and anti-sense strand, assemble transcripts, identify transcript boundaries, discover novel transcripts such as small RNAs
File search patterns
rockhopper:
contents: Number of gene-pairs predicted to be part of the same operon
fn: summary.txt
max_filesize: 500000