Reduced Represented Lib - Snp Calling In Unaligned Regions.
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9.6 years ago

Hi, we have a library of RRL sequences for a genome (tetraploid) that has not been assembled yet. The region of interest is 250 bases long, sequenced 72 BP single end. We are using 1 of its parent genome as a partial reference. We need to call the SNPs from the region which has not been aligned to our partial reference genome apart from the aligned region??? can some 1 suggest some tools that will help in the downstream analysis.

snp alignment • 1.8k views
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Entering edit mode
9.6 years ago

I don't completely understand. You have a partial reference, and you have SNPs from mapping to that, but you also have a load of stuff that doesn't map and you want to call markers in that?

The Cortex assembler can do this. In fact you might be interested in this related paper, just out. It's not directly applicable as they sequenced paired-end, but might be useful.

Reference-free SNP discovery for the Eurasian beaver from restriction site‚Äďassociated DNA paired-end data Helen Senn1,*, Rob Ogden1, Timothee Cezard2, Karim Gharbi2, Zamin Iqbal3, Eric Johnson4, Nick Kamps-Hughes4, Frank Rosell5, Ross McEwing1

Abstract In this study, we used restriction site‚Äďassociated DNA (RAD) sequencing to discover SNP markers suitable for population genetic and parentage analysis with the aim of using them for monitoring the reintroduction of the Eurasian beaver (Castor fibre) to Scotland. In the absence of a reference genome for beaver, we built contigs and discovered SNPs within them using paired-end RAD data, so as to have sufficient flanking region around the SNPs to conduct marker design. To do this, we used a simple pipeline which catalogued the Read 1 data in stacks and then used the assembler cortex_var to conduct de novo assembly and genotyping of multiple samples using the Read 2 data. The analysis of around 1.1 billion short reads of sequence data was reduced to a set of 2579 high-quality candidate SNP markers that were polymorphic in Norwegian and Bavarian beaver. Both laboratory validation of a subset of eight of the SNPs (1.3% error) and internal validation by confirming patterns of Mendelian inheritance in a family group (0.9% error) confirmed the success of this approach

http://onlinelibrary.wiley.com/doi/10.1111/mec.12242/abstract

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