Open jmtsuji opened 11 months ago
@jmtsuji Transferred this issue from https://github.com/rotary-genomics/rotary. What on this checklist has been completed?
@LeeBergstrand Updated -- thanks. Many of these items are still on the roadmap. The majority of them can be resolved once the next module I plan to write for rotary (which replaces more internal logic from circlator) is finished.
Tasks for
repair.py
and related code:circlator merge
parameters to better guarantee success of merging contigscirclator merge
params, then the default number oflength_threshold
iterations in the script can probably be decreased to save run time on complex samples.assembly_info.txt
file is used. Right now, only contigs in this file are analyzed. It would be better if the circular contigs in this file are treated as circular, but then all other contigs in the input FastA file are passed through the script as linear (rather than discarding contigs in the input FastA that aren't inassembly_info.txt
). The code will need to be refactored a bit to handle this.In the long term:
circulator merge
with in-house scripts to handle stitching the end-spanning contig onto the ends of the circular contigcirclator
paper), although I wonder if modern assemblers already handle these cases by default: e.g., checking to ensure that short circular contigs don't contain multiple repeats of the real contig sequence due to assembly issues