how can I get an interleaved fastq file from two pair-end seq files?

[tinyfallen]

Thanks a lot for your excellent tool !

[shenwei356]

seqtk mergepe : https://github.com/lh3/seqtk

mergepe   interleave two PE FASTA/Q files

[tinyfallen]

seqtk mergepe : https://github.com/lh3/seqtk

mergepe   interleave two PE FASTA/Q files

thanks for your timely reply！
best wishes ~

[mbhall88]

I know this functionality is handled by seqtk, but it would be awesome to have it included in seqkit so I don't have to install other tools - seqkit is the swiss army knife

Also, some functionality I am struggling to find elsewhere is the ability to interleave reads and add /1 and /2 suffixes

Here's my current solution...which is fine. But just wanted to say that I think this would be a nice addition to seqkit

tmp1=$(mktemp)
tmp2=$(mktemp)
# add /1 and /2 to read names
seqkit seq -i r1.fq | seqkit replace -p $ -r /1 > $tmp1
seqkit seq -i r2.fq | seqkit replace -p $ -r /2 > $tmp2
# interleave reads
seqtk mergepe $tmp1 $tmp2 > interleaved.fq

[tinyfallen]

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