454 Order Of Contigs Assembly And Mapping

Question

[Bdv]

we have a bacteria sequenced and assebled de novo, the reads were also mapped to a known reference. so we have contigs built de novo or contigs built according to a close reference. I would like to work with the de novo contigs but I need to knoe their order. Is it possible to combine somehow the data from the mapping and the de novo assembly?

Answer 1

[lexnederbragt]

I can recommend Mauve Contig Mover, it orders your contigs relative to a reference genome. http://asap.ahabs.wisc.edu/mauve-aligner/mauve-user-guide/reording-contigs-in-draft-genomes.html

[ALchEmiXt]

+1 for me. But reconsider that the algorithm used to find homology is slightly different from BLAST or BLAT. Its focus is on horizontal gene transfer (if I remember correct). Not saying that one of these is best. See what fits your question best, than pick your tool.

Answer 2

[ALchEmiXt]

What we and many others do is somthing like:

1. Map de individual contigs to the reference using BLAT or BLAST or similar. Just layout the contigs in order and use these as 'artificial' scaffolds. Synteny mapping we call it on our public galaxy instance.
2. Or if you have for instance paired-end or mate-pair information you can make an optimised scaffold de novo by mapping the pairs to the contigs and thereby determine the order and distance. Tools like SSPACE but there are probably more that can do that.

[Bdv]

thanks, where in galaxy is this synteny mapping? I saw only lastz and tools for illumina. I need for 454. ? thanks

[ALchEmiXt]

@bdv sorry. It is for option 1. The mapping of contigs to a reference using BLAT (BLAT/BLAST section). From BLAT generate the syntenylist (baiscally the orientation layout of contigs) which you can use subsequently to Join (you find it in the Artemis/MUMmer section) in an artificial chromosome using spacers and/or linker providing an EMBL layout file as well for inspecting in for instance ACT or Artemis of Sanger.