Mapping fastq files to reference genome

Question

[A_heath]

Hi all,

I have multiple fastq files of a bacterial genome obtained from Ox Nanopore sequencing.

I would like to map them against a reference genome that is very close. Then, ideally, I would like to assemble the mapped reads only using Flye.

What would be the most appropriate to map these sequencing data?

Thank you so much for your help!

Audrey

Answer 1

[hafiz.talhamalik]

try using GraphMap or minimap2

[A_heath]

Thank you for your help.

I indeed thought about these 2 tools but I don't think that I will be able to select mapped reads only...

[Sus]

I don't know GraphMap but minimap2 produces SAM files so you can use that (see here), it's very likely GraphMap also produces SAM or BAM files. Also if you want to choose your filters I recommend this little page from the picard documentation.