replacing perl script with shell command line

[Luke Florence]

Hi

I have been following the VSEARCH pipeline example script but run into issues when trying to run the perl script (mostly because I have no idea how to run perl and I can't get the map script to run!).

I was wondering if there is a way to run the 'Extract all non-chimeric, non-singleton sequences, dereplicated' and 'Extract all non-chimeric, non-singleton sequences in each sample' components of the script to get the 'all.nonchimeras.fasta' file using the shell command line?

Thank you in advance!

Luke

[Luke Florence]

Am I able to cluster OTUs straight from the 'all.ref.nonchimeras.fasta' file would I lose important information?

Cheers

Luke

[Luke Florence]

I have found an alternate map.pl script that works: https://github.com/telatin/vsearch_example/blob/master/map.pl