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QUAST alignment contig retrieval

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.

assembly genome alignment
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updated by Ram Ram • written by bpz • bpz

1 answer

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.
• 1 views • link
written by thackl thackl

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

• 0 views • link
updated by Ram Ram • written by bpz • bpz

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...

• 0 views • link
written by thackl thackl

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

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written by thackl thackl

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