Abra2 creating large (around 100bp) deletions to alignment
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rchapman2000 commented
Hello,
I have been using abra2 for viral reference based assembly for a while now and have not had any issues. However, recently I have noticed that in a few of my assemblies, there extremely large gaps being added in to the alignment by abra2. It appears that the tool is taking a few bases from the ends of a read and moving to a distant position. It is also odd because these regions do not contain any mismatches from the reference...
Below are screenshots of my alignment before and after running abra2.
I am currently running abra2 version 2.23 installed via conda.
Let me know what other information I can provide! Thank you!