Hello,
I've assembled some contigs from a sequenced strain and aligned them back to the reference with Mauve. I'm interested in studying those contigs that did not align. How can I extract those contigs?
Mauve can export a file with the positions of all those contigs in the input file so I can probably write a script to get the sequences, but I thought there's probably an easier way. Also, if you know a better software than Mauve, please tell me. My purpose is comparing several de-novo-assembled strains with each other and with the reference genome (~20MB) to see sequence variations.
Thanks!
I've assembled some contigs from a sequenced strain and aligned them back to the reference with Mauve. I'm interested in studying those contigs that did not align. How can I extract those contigs?
Mauve can export a file with the positions of all those contigs in the input file so I can probably write a script to get the sequences, but I thought there's probably an easier way. Also, if you know a better software than Mauve, please tell me. My purpose is comparing several de-novo-assembled strains with each other and with the reference genome (~20MB) to see sequence variations.
Thanks!
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