using Diamond for paired-end reads

Andrew Moffat

New member
Hello,

I am wanting to use Diamond for aligning Illumina paired-end reads. In the past I have always run both reads separately and dealt with the matching later, but I just noticed a command-line option `--strand query strands to search (both/minus/plus)`. Does this option mean that there is a way to input paired-end reads together? If I concatenate the two reads files, will Diamond match the reads by seqID?

Thanks,


Andrew Moffat
 
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