mafft --auto alignment
1
0
Entering edit mode
25 days ago
dbenig • 0

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 • 246 views
ADD COMMENT
1
Entering edit mode
24 days ago

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)

ADD COMMENT

Login before adding your answer.

Traffic: 1757 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6