This is a test version of Biostars. For the public version, visit https://www.biostars.org.
mafft --auto alignment

A newbie here.

I am trying to run mafft --auto input.fasta > output.aln for a few ONT .fasta files of genomic sequences.

I'm using a bash script to perform mafft alignment on all .fasta files in the working directory, but the command is taking ages to execute and I'm wondering if * and ? in the files are causing the delay. Or is it just the sizes of the files that are causing the delay.

Any feedback, comment, or suggestion regarding this issues would be appreciated.

Thank you

--auto alignment mafft
• 1,222 views • link
updated by Max Sikolenko • Max Sikolenko • written by dbenig • dbenig

1 answer

Well, multiple sequence alignment would be a long task to complete for large datasets. So, if you align many sequences (say, more than 1000), and/or they are long (say, longer than 5–10k bp), then the delay isn’t surprising at all.

(And “ONT” in your question sort of suggests that you have much data)

• 0 views • link
written by Max Sikolenko • Max Sikolenko

Log in to answer this question.

More posts like this