Understanding pilon correction on the reference sequence
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11 months ago

Hello,

I need some clarification about specific kind fix made by pilon on the reference sequence:

ref             -GGAGTGCTCCGGGCGGGTGACCCGGCACCACCACGACAGCGCCTGCTGCTGTGGACCGA
fix             CGGAGTGCTCCGGGCGGGTGACCCGGCACCACCACGACAGCGCCTGCTGCTGTGGACCGA
***********************************************************

ref             TCAGCTGGTCCGGTTCCCGAAGGTGACTGTCTCGCAGCGTGGTCGCGTCGTCGCGACCAC
fix             TCAGCTGGTCCGGTTCCCGAAGGTGACTGTCTCGCAGCGTGGTCGCGTCGTCGCGACCAC
************************************************************

ref             GCTGCTGCCCTGGGCCGCCTCACCGGGACGGGTCTTCCGGGTGCCGTGGTCGATCATGGA
fix             GCTGCTGCCCTGGGCCGCCTCACCGGGACGGGTCTTCCGGGTGCCGTGGTCGATCATGGA
************************************************************

ref             CGCCGTCGACCCGGCACTGGGGCCCGTGACCGTCGGACTGGCCAACGCACCTCGTCGGGG
fix             CGCCGTCGACCCGGCACTGGGGCCCGTGACCGTCGGACTGGCCAACGCACCTCGTCGGGG
************************************************************

ref             AACCACGCCCAATGCGGTCGGGGAATTCATTCCCTCCCGCTGCAACTGAGCACACCCCCG
fix             AACCACGCCCAATGCGGTCGGGGAATTCATTCCCTCCCGCTGCAACTGAGCACACCCCCG
************************************************************

ref             ACACGCACTCTCGTTCAGCACTACCCCGCACACAGATTGTCGACAGTAAACTTCGATCGA
fix             ACACGCACTCTCGTTCAGCACTACCCCGCACACAGATTGTCGACAGTAAACTTCGATCGA
************************************************************

ref             TCGGAAGACACATGACGGAAGTACAGGGCGGTTTGCACGGTCCCGAGATGCGGCGGGCCA
fix             TCGGAAGACACATGACGGAAGTACAGGGCGGTTTGCACGGTCCCGAGATGCGGCGGGCCA
************************************************************

ref             TCACGGCCGCCGCGATCGGAAACTTCATCACCTGGTTCGACTTCGCGGCATACGGATTTC
fix             TCACGGCCGCCGCGATCGGAAACTTCATCACCTGGTTCGACTTCGCGGCATACGGATTTC
************************************************************

ref             TCGCCGTCCTGCTCGGCCAGATCTTCTTT-
fix             TCGCCGTCCTGCTCGGCCAGATCTTCTTTC
*****************************


In the example above ref and fix are identical except the first and last bases. My question is: why is this fix not reported as two independent nucletide insertion? It is possible that what I am looking at is a local misassembly?

Thanks

pilon • 445 views
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It might be that the "fix" is that pilon extended the contig with two bases: a C on either end of the contig.

(technically that would probably not indicated as 'insertion' but rather as 'extension' , I would think)

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Those changes actually happen on a scaffold of several Mbp.

I will post the same question on https://github.com/broadinstitute/pilon in case someone has the same doubt.

It is not important, but for some odd reason it really bugs me