gmap gsnap loop

Hello,

What is an appropriate loop for gmap gsnap alignment syntax for ~20K reference genomes? Essentially, I would like gmap gsnap to run through each genome independently and output results?

assembly next-gen alignment

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written 6.1 years ago by Ada •

Like an example loop shown here: A: How to run BWA or the other aligner for paired .fastq in a bash loop and pipelin

You may need to do a nested loop (two for loops) if you want to align every sample file to every reference.

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written 6.1 years ago by GenoMax

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