Improve assembly quality with BAC sequences

[Björn_P.]

Hello everybody,

I am trying to improve my current assembly with some BAC sequences. I therefore thought of "scaffolding the scaffolds" and taking the BACs as an additional input data.

My data:
- 1800 scaffolds with an N50 of 3.6mb
- 50 BACs with a length of 120kb

I first wanted to use an assembler like Newbler or CARBOG, or a scaffolding program like Bambus or SSPACE, but they can't handle the input sizes or Ns in the data.

I also thought of using some BLAST version (maybe MEGABLAST) to map the BACs to the Scaffolds, but im not sure if this will work.

Has anyone any suggestions or hints?
Thank you very much!

Regards Björn

[boetsie]

You might want to try to align the scaffolds to the BACs with nucmer (part of the MUMmer package: http://mummer.sourceforge.net/). The command would be;

nucmer <BAC-sequences> <scaffold-sequences> --coords -p <output-prefix>

Look in the file <output-prefix>.coords where the alignment of the scaffolds against the BACs is shown in the order along the position of the BAC. With this information you can show the order of your scaffolds along the genome.

Regards,
Boetsie