Adapt RAMPART's demuxing to use qcat.

artic-network / rampart

Read Assignment, Mapping, and Phylogenetic Analysis in Real Time

GNU General Public License v3.0

79 stars 33 forks source link

Adapt RAMPART's demuxing to use qcat. #24

Closed rambaut closed 5 years ago

rambaut commented 5 years ago

Plan to switch from modified version of porechop to using off-the-shelf qcat (https://github.com/nanoporetech/qcat). Need to assess the best way of doing this (i.e., do we still put barcode calls into the read headers).

rambaut commented 5 years ago

The modified version of porechop put the barcode call into the header. qcat does this by default (i.e., barcode=6 or barcode=none). Should be easy to move over.

rambaut commented 5 years ago

Currently qcat doesn't support double barcode checks? The --dual option results in no barcodes being detected.

rambaut commented 5 years ago

Closing this issue because the plan is to decouple RAMPART from the method of demuxing.