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broadinstitute / pilon

Pilon is an automated genome assembly improvement and variant detection tool
GNU General Public License v2.0
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Asymmetric mapping in two repeat areas #121

Open YiweiZhu opened 4 years ago

YiweiZhu commented 4 years ago

Hi everyone! I am polishing a Nanopore assembly with Illumina short reads via pilon. On one contig, it is assumed to be two inversed repeats. As illustrated by the variable scale in the coverage plot, Illumina reads are attributed to either region asymmetrically. The low-covered areas in the repeats are covered barely with Illumina reads (green arrows), while the high-covered area are of twice the mean coverage (red arrows). The asymmetric mapping has caused pilon fail to fix base assembly errors in the low-covered area. Iterating pilon polishing steps hardly help solve this problem, since it only fixes errors in high-covered area and leaves those in low-covered area showing “NoSolution” in each round. Is it proper to tweak aligner’s parameters to tolerate the second-best aligned location so that pilon can fix errors in both of the repeat areas? BAM示意图

cfz1998 commented 1 year ago

Hi!@YiweiZhu. I have the same error. Do you know how to fix it?

Thank you for you reply!

YiweiZhu commented 1 year ago

Sorry, no solution yet. @cfz1998

cfz1998 commented 1 year ago

Sorry, no solution yet. @cfz1998

NextPolish also has this issue. How about using PacBio HIFI to assemble these repeat regions?

YiweiZhu commented 1 year ago

I never used PacBio before. Maybe you can have a try. As far as I know, one concern of PacBio for repeat regions is whether the reads could be longer than a repeat unit, since PacBio reads are not so long as those of Nanopore.

cfz1998 commented 1 year ago

Thank you very much!