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Short error-prone alignment #135

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armintoepfer opened this issue Mar 22, 2018 · 2 comments
Closed

Short error-prone alignment #135

armintoepfer opened this issue Mar 22, 2018 · 2 comments
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@armintoepfer
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armintoepfer commented Mar 22, 2018 •
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I'm trying to use minimap2 to cluster short pacbio insertions from raw subreads. I've had no success in finding the right parameter combination to get the alignment of those two fragments:

ATGACCCCCCACAGCTTTACCCACGCCACACACAGATCAGATCTGACTCAGGCTCTTTACTGAATCAGC
ACCCCCCACAGCTGTACCCAGCGCCACACACAGAGCAGACGCTGGAACACTGTTATTGAAGGAATCAGCAATGGGGTA

A naive SW gives me following result:

ATGACCCCCCACAGCTTTACCCA-CGCCACACACAGATCAGAT-CTGACTCAGGC-TCTTTACTGAATCAGC---------  81
   ||||||||||||| |||||| ||||||||||||| ||||  |||   ||    | || |  ||||||||         
---ACCCCCCACAGCTGTACCCAGCGCCACACACAGAGCAGACGCTGGAACACTGTTATTGAAGGAATCAGCAATGGGGTA  81

Btw, I'm using the C API, so internal hacks are possible :)
@lh3 lh3 added the question label Mar 22, 2018
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lh3 commented Mar 22, 2018

I wouldn't recommend to use minimap2 for short noisy matches, but if you would like to do that anyway (reduce -k if you want even higher sensitivity):

./minimap2 -c -k11 -w1 -n2 -m10 -s20 first.fa second.fa

@lh3 lh3 closed this as completed Mar 22, 2018
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lh3 commented Mar 22, 2018

The command line above truncates the second half of the alignment. You may reduce the mismatch penalty to save that:

./minimap2 -c -k11 -w1 -n2 -m10 -s20 -B2 first.fa second.fa

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