using Diamond for paired-end reads

Andrew Moffat

New member

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?


Andrew Moffat