Modifying FASTQ header

Question

[SaltedPork]

My FASTQ header:

@M03972:198:000000000-CJVFC:1:1101:13861:2151 1:N:0:TAGCGCTC+GCGTAAGA

Desired FASTQ header:

@M03972:198:000000000-CJVFC:1:1101:13861:2151/1

There are two steps I wish to perform, the first is to remove the extra Illumina details after the ' 1', the second is to convert ' 1' to '/1'.

1. Are there any programs available that can do this? I have looked at Seqkit and FASTX-Toolkit, neither do what I am after.

2. I have considered using sed commands, with the regex :N:0:\w+\+\w+ Is there a better command?

Answer 1

[GenoMax]

Using BBMap suite:

$ more test.fq
@M03972:198:000000000-CJVFC:1:1101:13861:2151 1:N:0:TAGCGCTC+GCGTAAGA
ACGATCGAGC
+
IIIIIIIIII

$ reformat.sh -Xmx2g in=test.fq out=stdout.fq trd=t | reformat.sh -Xmx2g in=stdin.fq out=final.fq addslash=t int=f

Will produce

@M03972:198:000000000-CJVFC:1:1101:13861:2151 /1
ACGATCGAGC
+
IIIIIIIIII

replace test.fq with your own file.

Answer 2

[rpolicastro]

seqkit answer

seqkit replace -p "(^\S+)\s([0-9]+).+" -r '$1/$2' file.fastq

Answer 3

[Zhitian Wu]

I think there is no right or wrong with your :N:0:\w+\+\w+, if it works, then just use it.

• you might want to use [ATCG]+ instead of \w+
• you can add $ at the end for anchoring