An option to output SEQ field for secondary alignment #687
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
|
It would be really great if this patch could be applied to enable building flye smoothly. |
|
Hi all, Will be happy to make this pull up-to-date with the master, once you confirm that you are interested in adopting. The conflict is due to new command line options, so it is an easy fix. |
|
@fenderglass, |
|
just saw this PR but I made a program that tries to help add SEQ to secondary alignments as a post-processing step though this PR would be interesting too! https://github.com/cmdcolin/secondary_rewriter |
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Outdated suggestions cannot be applied.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.
Hi!
I have been using minimap2 as a part of the Flye pipeline. I am using secondary alignments during consensus/polishing to account for possible duplications in disjointigs and improve the base quality of long repeats. Storing SEQ field for secondary alignments in SAM/BAM files makes the alignment file parsing much easier, since all separate alignments could be processed independently.
An existing
-Yoption solves the problem, but it also forces supplementary alignments to use soft clipping, which in some datasets dramatically increases alignment size. I therefore added a new option-secondary-seqthat enables output of SEQ for secondary alignments, and uses hard clipping for both supplementary and secondary alignments.The option was extensively tested as a part of the Flye pipeline for almost a year. I however have not tested outside of genome assembly setting.
Best,
Mikhail