New release of the Read Assembly and Annotation Pipeline Tool (RAPT), now 2X faster!

There is a new release of the Read assembly and Annotation Pipeline Tool (RAPT) available from our GitHub site. RAPT is a one-step application for the genome assembly and gene annotation of archaeal and bacterial isolates that can run on your local computer or the Google Cloud Platform (GCP). With this new release, jobs will run twice as fast as with the December release. For example, we have assembled and annotated a Salmonella enterica genome in under an hour on a 16-CPU machine with the new release.
We have also added several new features based on your feedback including:

  1. The –stop-on-errors flag that will stop the process if there evidence from the average nucleotide identity check that there is sample mix-up or contamination by other bacteria.
  2. The ability to accept forward and reverse reads of paired-end runs in separate files. These can be compressed (gzip) files.

Finally, thanks to all who came to our webinar in December and provided their comments! For these who couldn’t join us, you can now view the recording on our YouTube channel.

Contact us at prokaryote-tools@ncbi.nlm.nih.gov with any question and to let us know if you would like to become a beta-tester for RAPT.

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