Open Adamtaranto opened 10 months ago
Proposed modules names:
teloclip filter teloclip extract teloclip extend
Need to balance convenience vs enabling errors.
Could provide tutorial on manual curation: Select the best overhang-read (i.e. confident anchor region, unique alignment, many reads agree) and then extend contig with teloclip extend
.
Alternatively, could provide an extend-now-ask-questions-later option whereby we extend contigs using the longest available overhang and then suggest validation checks i.e. align all overhang-reads back to the extended contig and look for agreement between reads.
Add output option for extract
to yield MAF or MSA of overhang-reads that can be viewed in terminal or externally.
Note: Log total bases extended and bases per contig end. Useful for reporting results.
Option: Output BED file coords for extended sequence segments for review.
Existing modules:
New module:
Tasks: