Question: Amplicon Seq analsis from MiSeq mulpilxed barcoded short reads
22 months ago by
fola.a • 0
fola.a • 0 wrote:
I am working Plasmodium Genome. My project mainly focuses on short Amplicon sequence using Miseq platform and I have a total of 200 primers designed for targeted 200 loci on 14 chromosomes. I would like to ask you which pipeline would be better to 1. demultiplex based on primers/ sample 2. Quality filter 3. Mapping reads 4. Variant calling simultaneously. Since the majority of current pipelines (GATK and others) were designed for large reads and diploid organism like human. Any suggestion or comment highly appreciated for my data (short millions of multiplexed reads for a haploid organism)...
With Regards, Abe