Increase the allowed minimum overlap length #404
Closed
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
With very long ONT reads and sufficient coverage, using a larger -m than the allowed default seems to produce better assemblies with fewer contigs in some cases than just prefiltering input reads by length, which also prevents shorter reads from contributing to polishing. It looks to me like the 10Kbp upper bound was arbitrary, and I don't haven't seen an indication of unexpected side effects of using values here like 20Kbp. Of course, increasing this parameter leads to lower coverage during graph construction, just as with prefiltering input reads.
|
Minimum overlap parameter does not affect polishing. Unless there is any evidence of better assemblies minimum overlap >10k, I'd rather stick with the tried-and-tested parameter settings. |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
With very long ONT reads and sufficient coverage, using a larger -m than the allowed default seems to produce better assemblies with fewer contigs in some cases than just prefiltering input reads by length, which also prevents shorter reads from contributing to polishing.
It looks to me like the 10Kbp upper bound was arbitrary, and I don't haven't seen an indication of unexpected side effects of using values here like 20Kbp. Of course, increasing this parameter leads to lower coverage during graph construction, just as with prefiltering input reads.