Merging Multiple De Novo Assembly Fasta Files
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10.6 years ago
rob234king ▴ 610

I have a series of assemblies in fasta format from SOAP2 using different k values. I would like to merge the resulting assemblies to one file because some k values assemble parts that others don't, to create hopefully larger contigs. I thought I might be able to use oases to merge the files as this is what happens for the velvet/oases transcriptome assembly but not sure how I could do that. The commands don't appear to lend themselves to this application. Any ideas would be welcomed. I also have another three re-sequencing assemblies of different k values which could also try merging to this one re-sequencing data set.

A reference exists although as ~30 contigs, some are very large so it's quite good (there should be only four chromosomes in the genome).

I don't want to manually try to do this, I have already manually plugged some large N gaps in the first reference contig but too time costly and have not looked to stick contigs together yet either.

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you can have a look https://github.com/ghyao/GAA

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thanks, I've been looking around and looks like the most user friendly and maybe use it to merge one good assembly with the reference and hopefully it will at least replace the N's in the reference sequence.

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Please let me know the performance of GAA

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I cant understand why this program needs contigs to be named in a certain fashion. The contigs from 2 different assemblies are completely unrelated in order or naming.

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10.6 years ago

Minimus2 ?

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Looks like may be useful with multiple rounds of merging two files but looks like would have to install the whole amos package. I'll give the installation a try and see if works. Thanks

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Had to convert the configure file to linux and then ran but got below error? any ideas? error: cannot run /bin/sh config/config.sub

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