454 reads correct with illumina

biocomfun · 09-10-2011, 10:30 AM

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 · 09-13-2011, 08:01 AM

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 · 09-14-2011, 02:21 AM

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 · 01-23-2012, 03:57 PM

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 · 01-29-2012, 05:27 PM

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 · 02-11-2012, 01:29 AM

Quote:

Originally Posted by 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 .

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 · 02-12-2012, 04:00 AM

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

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09-13-2011, 08:01 AM	#2
colindaven Senior Member Location: Germany Join Date: Oct 2008 Posts: 415	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.

09-14-2011, 02:21 AM	#3
biocomfun Junior Member Location: china shenzhen Join Date: Sep 2011 Posts: 6	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 !

01-23-2012, 03:57 PM	#4
jnfass Member Location: Davis, CA Join Date: Aug 2008 Posts: 88	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?

01-29-2012, 05:27 PM	#5
biocomfun Junior Member Location: china shenzhen Join Date: Sep 2011 Posts: 6	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 .

02-12-2012, 04:00 AM	#7
biocomfun Junior Member Location: china shenzhen Join Date: Sep 2011 Posts: 6	you can send a mail to the ahthor ! Good luck !