Using Minimap2 with FMLRC2

Question

[jwalewski]

Hello all,

I am using FMLRC2 (https://github.com/HudsonAlpha/rust-fmlrc) to correct PacBio reads with Illumina reads for hybrid genome assembly. Since FMLRC2 only corrects reads (does not do any assembly) another program is needed. In the paper published on FMLRC minimap (now succeeded by minimap2, https://github.com/lh3/minimap2) was used, followed by miniasm, for the actual assembly.

FMLRC2 outputs one fasta file (of the corrected long reads), yet, on minimap2's github page, I only see options that involve 2 or more input files.

How is minimap2 used in combination with FMLRC2?

Many thanks for your time,

Joe

Answer 1

[liorglic]

The answer is in the Miniasm github page. You simply specify the same reads file twice, like this:

minimap2 -x ava-pb  corrected_reads.fa corrected_reads.fa > all_vs_all.paf