From Contigs To Chromosome Scale Scaffold

Question

[Jianguo Lu]

I have a whole genome sequencing project. We got 50X Illumnia draft sequences and then we did the assembly. We got over 3 million contigs, the N50 value is around 6kb. Next step is too close those gaps as many as we can. We want to use our huge previous data, including EST, BES, Physical map, Linkage map, SNP, and full length cDNA, to reduce those gaps. So, is there any good protocols or good bioinformatic tool we can use to do this? Appreciate it!

[Leszek]

what program you used to get contigs? what organism is it, or at least family or genome size? do you have any close sequenced species?

Answer 1

[2184687-1231-83-]

One option is to use IMAGE: http://genomebiology.com/2010/11/4/R41

[Haibao Tang]

For IMAGE to work, one has to order the contigs first, so a scaffolder, such as SOAPdenovo needs to be run first.

Answer 2

[Leszek]

SOAPdenovo works fine with scaffolding using paired-end information only. I've tried it with fungal genomes (20-30Mb). If you have close species that is well assembled, you can try Oslay to get supercontigs/chromosomes.