QUAST alignment contig retrieval

Question

[bpz]

Hello everyone

I have used QUAST to analyze a set of contigs against a reference genome, and one of the results is an image (svg) of the alignment of my contigs and the reference. Does anyone knows if I can retrieve such alignment in a fasta format?

Thanks a lot.

Answer 1

[thackl]

Not sure if you can extract that from quast output, but to my knowledge, quast uses MUMmer for the genome alignments. You should be able to run MUMmer directly to get your desired output.

[bpz]

Hello

Thanks a lot for the advice. I am running MUMmer now... but I can't find any commnads to obtain a fasta output. Any ideas on how can I achieve this?

Cheers

[thackl]

That indeed is a very good question - I just assumed that mummer can do fasta output, though after browsing the manual, I don't really know, if it is possible...

[thackl]

The closest thing to FASTA that mummer can generate, seems to be the show-aligns output... Not sure if that helps, sorry...