Washington University School of Medicine SNP Research Facility
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FP-TDI SNP genotyping


SNP Discovery in C. briggsae (build 2)

Important: There has since been a new release of C. briggsae SNPs.

Sequence Traces
We obtained 13,632 sequence traces from Washington University's Genome Sequencing Center. These were random reads from the HK104 strain of C. briggsae; discovery was performed using the canonical AF16 sequence as a reference.

SNP Discovery Algorithms
Three separate methods of SNP discovery were independently applied to the trace set; their results were combined. Our "control" method simply used CrossMatch to align reads to the canonical sequence, identifying any mismatches above a certain quality threshold to be polymorphisms. The second method utilized Polyphred, a suite of tools including Phrap, Phred, and CrossMatch from the University of Washington. The final SNP discovery method utilized was SahaSNP, which was generously applied to the trace set by Jim Mullikin.

SNP Discovery Results
method discovered snps
CrossMatch (control) 21,243
Polyphred (Univ. of Washington) 18,182
SahaSNP (Jim Mullikin) 19,485

C. briggsae SNPs
The link below is to a tab-delimited text file containing 26,488 C. briggsae SNPs discovered using Polyphred and SahaSNP. Click to view the text file, or right-click and select "Save Target As" to download. You can also view SNPs by super contig in your web browser.

Download:   HK104 SNPs (build 2)

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