BFC and read pairing infoΒΆ

There is what I consider a bug in bfc, read pairing information is stipped when using bfc to correct fastQ reads in the Illumina 1.8 format or newer. This has been described here: and

The bug requires, assuming you want to interleave and de-interleave reads, which I think most people will want to do, that you place the /1 and /2 tags in the fastQ headers. To do this, follow the below steps.

sed 's_ _/1 _g' file.1.fq > edited_file.1.fq

and to for the /2 read file

sed 's_ _/2 _g' file.2.fq > edited_file.2.fq

Then supply the edited files to seqtk for merging, bfc for correction, and so on...