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General: Assembly
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nkravit
Jul 26th 2010
When I assemble my sequences, the contig always takes some reads, inverts them, and assembles them into a repeat that's not really there. I have several questions with regard to this. Can I search a contig for repeats? If I download and install the MAFFT plug in, will it run automatically? I don't see a way to specifically select it for assembly. I'm not really a bioinformatics type, so what settings can I put into Geneious to prevent false assemblies? So far, I still get this problem with the high sensitivity assembly parameters.

Thanks for any help!
Matt Kearse
Jul 26th 2010
MAFFT is a multiple alignment tool rather than an assembler. If you install it you can use it in Geneious from the alignment button.

Are you trying to do a reference sequence assembly or de novo assembly? If you believe the assembler is giving incorrect results would you mind sharing your data with us so we can see what is happening and suggest a fix.
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