Hi all! [SNP calls from Illumina w/o reference]

gdilla · 08-13-2010, 01:29 PM

Hey,
I'm working on getting SNP calls from Illumina data in a plant with no reference genome in order to infer population structure.

I'm using restriction-site associated DNA (RAD loci) as a complexity reduction step (Samples are digested then size-selected to get an arbitrary but reproducible fraction of the genome). I'm also using multiplexing to get the sample size up.

So far I've been using ABySS to assemble the reads into mini-contigs (contig length = read length), then MAQ to map the reads back to the contigs, and finally custom scripts to call the SNPs.

If anyone has suggestions on other bioinformatic strategies, I'd be happy to hear them! (I've been looking at SOAP, Mira, CLC, velvet)

Thanks for all the useful posts in the archives!
G

Code:

Genome            -----------------------------
Restriction sites    *       *           * 

        Plant_1     = =     = =         = =  
Reads               = =       =         = =
        Plant_2     = =     = =         = + 
                    = =     =             + 
                                        (SNP)

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Impact on quality of SNP calls using samtools mpileup	myi	Bioinformatics	3	03-03-2014 08:18 AM
None reference heterozygous calls	Chiel	Bioinformatics	0	01-03-2011 05:34 AM
Supporting Reads in SAMTools SNP Calls	Lee Sam	Bioinformatics	2	07-09-2010 07:16 AM
maq 2nd and 3rd likely SNP Calls	AnamikaDarwin	Bioinformatics	0	07-24-2009 09:00 AM
Maq SNP calls from a large pool	mimi_lupton	Bioinformatics	0	10-31-2008 09:48 AM

08-13-2010, 01:29 PM	#1
gdilla Junior Member Location: Chicago Join Date: Aug 2010 Posts: 1	Hi all! [SNP calls from Illumina w/o reference] Hey, I'm working on getting SNP calls from Illumina data in a plant with no reference genome in order to infer population structure. I'm using restriction-site associated DNA (RAD loci) as a complexity reduction step (Samples are digested then size-selected to get an arbitrary but reproducible fraction of the genome). I'm also using multiplexing to get the sample size up. So far I've been using ABySS to assemble the reads into mini-contigs (contig length = read length), then MAQ to map the reads back to the contigs, and finally custom scripts to call the SNPs. If anyone has suggestions on other bioinformatic strategies, I'd be happy to hear them! (I've been looking at SOAP, Mira, CLC, velvet) Thanks for all the useful posts in the archives! G Code: Genome ----------------------------- Restriction sites * * * Plant_1 = = = = = = Reads = = = = = Plant_2 = = = = = + = = = + (SNP)