GBS paired reads splits it into several smaller files based on barcode matching

Question

[nakanomasayuki265]

I wanted to split demultiplexed paired-end Fastq files into individual data based on barcode matching. I know that single-end reads could be divided using FASTX-Toolkit, but not paired-end reads. Please tell me how to split demultiplexed paired-end Fastq files. Only R1 reads contain the barcode.

[cpad0112]

did you try GBSX tool? nakanomasayuki265

Answer 1

[rimgubaev]

Actually, I am dealing with the same problem, can't find a proper solution. I found this package but didn't try it yet: https://sourceforge.net/projects/gbsbarcode/files/

Answer 2

[Corentin]

I used this tool before to split GBS reads: https://sourceforge.net/projects/gbsbarcode/

It support paired end reads

Answer 3

[rimgubaev]

Tried this tool: https://github.com/kdmurray91/axe Works fine!