454 reads correct with illumina

[biocomfun]

by 454 and illumina reads assemble 300m genome :

my schedule is
1 correct the 454 reads by illumina 90bp reads by Coral (the attachment)
2 assemble by celera or newbler

do you anyone have done it ? is there another way to do it ?

[colindaven]

We tried one called Nesoni to correct bacterial 454 contigs using Illumina short read data. It worked ok and corrected about 50 errors in a 6MB genome (if I remember rightly).

We haven't continued with this approach extensively, your 300 MB sounds like a lot more of a challenge.

[biocomfun]

yeah,thanks a lot ,i have done the work by Coral ,and assemble with the software Newbler,it has a great improve for genome size .
for my genome is highly heterozygosis, i think it is useful !

[jnfass]

Can I ask, biocomfun, how you used CORAL to correct 454 reads using Illumina reads? As far as I can tell, CORAL simply takes a set of reads and does multiple alignment ... i.e. you can't specify a set of reads to be corrected and a different set of reads to be trusted and used for correction. What did you do, merge your 454 and Illumina reads into one fastq file?

[biocomfun]

I use 30x solexa reads to correct 10x 454 reads specifically,with a improved version of Coral by author,it can specify a set of reads to correct with a different sets of data .

[Kakadua]

I use 30x solexa reads to correct 10x 454 reads specifically,with a improved version of Coral by author,it can specify a set of reads to correct with a different sets of data .

I'm interested in what you mean by this, how does this work? I plan on using Coral for my current de novo project. Is it possible to obtain this per-released version of Coral?

/andreas

[biocomfun]

you can send a mail to the ahthor ! Good luck !