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Rockhopper

note

Bacterial RNA-seq analysis: align reads to coding sequences, rRNAs, tRNAs, and miscellaneous RNAs.

https://cs.wellesley.edu/~btjaden/Rockhopper/

DOI: 10.1016/j.ymeth.2019.03.026, 10.1186/s13059-014-0572-2, 10.1093/nar/gkt444

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
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