How to combine and convert fastq PE files into fasta files as batch?

Question

[sunnykevin97]

HI

I had ~ 100 PE fastq files, I wish to convert them into fasta file separately.

(ex. R1 , R2 ---> fasta file, for each set.

How I do ? not able to find any bash script, need suggestions!

[WouterDeCoster]

Please show some more effort in solving the problem before asking us, and show us what you have tried. This is a veryggeneral task for which you should be able to find a solution with minimal searching online. For sure there are many questions about this already on biostars.

You need to find a tool (like seqkit, or find many other options through Google) that can do this operation for a single file. Next step you either need to write a bash loop or use a parallelization program such as gnu parallel. For both of these you can find lots of useful resources to help you online, and you can ask us a more specific question if you get stuck.

Answer 1

[ashish]

See reformat.sh from BBtools. The page also tells you how to run it in loop.