I am working with a alignment file of more than 10,00,000 sequences of ~1500 in length. My task is to chop out the sequences by keeping only the first 700 bases. I have tried the chop.seqs provided in mothur package, but its taking too long as the data is huge. Is there any way to include the parameter of ‘Processors’ in chop.seqs (like in the other commands: align.seqs, filter.seqs), Please suggest.
Thanks for the suggestion. This will be part of 1.27.0.