How to deal with paired-end Illumina reads

[473021677]

Hi:
I am trying to use crass v0.3.6 to recover CRISPR spacer and repeat elements from metagenomic reads but I have encountered one problem. The metagenomic reads were generated by Illumina paired-end sequencing. So should I merge the two fastq files before I run crass? I will be eagerto get your guidance. Thanks very much.

Best regards,
YangYuan

[ctSkennerton]

Unfortunately crass doesn't use any of the read pair information however you don't need to merge the files. Crass can be given multiple files like crass file_read1.fastq.gz file_read2.fastq.gz and it will process both of them