mapping long-reads to a reference library

Question

[mthm]

Hi,

I have long, pacbio, reads and I have a reference library of only repeats, I want to map the long reads on the repeats library using bwa mem, is this command correct?

bwa index mmm.pacbio.fastq.gz
bwa mem mmm.pacbio.fastq.gz  repeat-library.fasta | samtools sort -@16 -  -o mm.vs.lib.sorted.bam

Do I need reference genome for mapping?

Answer 1

[ATpoint]

You need to index the reference genome, not the fastq files. I think for long reads people prefer minimap2 though these days.

what is the purpose of indexing a genome

Please see the manuals of bwa-mem or minimap2, it explains what to do.

https://lh3.github.io/minimap2/minimap2.html

http://bio-bwa.sourceforge.net/bwa.shtml