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Nextomics / NextPolish

Fast and accurately polish the genome generated by long reads.
GNU General Public License v3.0
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Using Mate-paired reads #56

Closed rmarquezp closed 4 years ago

rmarquezp commented 4 years ago

Hello, I am polishing a genome assembly using a combination of paired-end and mate-paired Illumina reads. Is it necessary to re-orient the mate-paired reads (which are oriented as RF instead or FR as in paired-end)? From the Bioinformatics paper it seems like NextPolish doesn't use pairing or orientation information, so reorienting should not be necessary, but I wanted to confirm.

Thanks!

moold commented 4 years ago

Hi, you can not combine paired ends and mate-paired reads for polishing. Because NextPolish will use the head ~50,000 reads to estimate the insert size, and use this insert size to filter the mapped reads. Therefore mate-paired reads may be filtered because their insert size is much larger than the paired end reads.

rmarquezp commented 4 years ago

Got it, thanks!