Question: From Contigs To Chromosome Scale Scaffold
1
gravatar for Jianguo Lu
7.8 years ago by
Jianguo Lu200
Auburn, AL
Jianguo Lu200 wrote:

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!

ADD COMMENTlink modified 7.7 years ago by Leszek4.0k • written 7.8 years ago by Jianguo Lu200

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?

ADD REPLYlink written 7.7 years ago by Leszek4.0k
4
gravatar for 2184687-1231-83-
7.8 years ago by
2184687-1231-83-4.9k wrote:

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

ADD COMMENTlink written 7.8 years ago by 2184687-1231-83-4.9k
1

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

ADD REPLYlink written 7.7 years ago by Haibao Tang3.0k
2
gravatar for Leszek
7.7 years ago by
Leszek4.0k
IIMCB, Poland
Leszek4.0k wrote:

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.

ADD COMMENTlink written 7.7 years ago by Leszek4.0k
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