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ctSkennerton / crass

The CRISPR assembler
http://ctskennerton.github.io/crass
GNU General Public License v3.0
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How to deal with paired-end Illumina reads #97

Closed 473021677 closed 4 years ago

473021677 commented 4 years ago

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 commented 4 years ago

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