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Month: November 2017

Get reads which map completely to reference using minimap (PacBio & Oxford Nanopore)

Get reads which map completely to reference using minimap (PacBio & Oxford Nanopore)

Minimap is a tool to find approximate mapping positions between two sets of long noisy reads or between genomes and long noisy reads like PacBio of Oxford Nanopore data (https://github.com/lh3/minimap). Standard output is in PAF format (https://github.com/lh3/miniasm/blob/master/PAF.md). If you want to filter the PAF file for reads which map entirely (or close to complete) to a genome you can use this simple awk command: awk ‘{if(($4-$3)>(0.9*$2)) print}’ mapping.paf > mapping.filtered.paf Nothing fancy at all. But it might help for example…

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