fastq.gz splitter tool

Question

[singh.bioinfo]

Hey everyone,

I want to split fastq.gz file because its too big to deal it. Please give me suggestion how to solve this problem.

Thanks,
Sakshi

Answer 1

[Bastien Hervé]

You have fasta or fastq files, it's not clear with your fastaq.gz. In any way you can use this command line :

zcat your_file.fastq.gz | split -l 10000000 - prefix

You will get files like prefixaa, prefixab, prefixac... All files will have 10000000 lines

Answer 2

[GenoMax]

reformat.sh from BBMap suite (check sampling parameters).

[Istvan Albert]

for BBMAP I find this version of the docs very helpful

https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbmap-guide/