is there a tool to recover corrupted fastq files

Question

[pt.taklifi]

So I have several fastq files of a BS-seq assay and most of them are corrupted, some reads either don't have a header or the third line (the line with + ), since the files are quiet large, I don't think I could recover them with typical commands in linux. So I was wondering if there is a tool that removes only the corrupted reads.

Thanks in advance

Answer 1

[rpolicastro]

You can use seqkit sana to remove malformed entries, and optionally seqkit pair afterwards if it's paired end data to match up the remaining read pairs.

Answer 2

[Tommaso]

You may also want to give a try to FastqWiper (https://github.com/mazzalab/fastqwiper)