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Old 08-22-2011, 01:59 PM   #3
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Location: San Francisco, CA

Join Date: Jun 2011
Posts: 9

Unfortunately Bowtie is not optimized for Complete Genomics data. Specifically, Complete Genomics reads have sub-read gaps that Bowtie will interpret as mismatches. The high mismatch frequency will prevent Bowtie from successfully aligning many reads to the reference.

If you are interested in working with SNP genotypes and Complete Genomics data, we strongly recommend using the Complete Genomics-developed snpdiff command in our open source CGA Tools package ( This tool is specifically designed to extract SNP genotypes from Complete Genomics data, and to compare Complete Genomics genotype calls with SNP genotypes generated on other platforms.
Shaun Cordes, PhD | Customer Support Scientist | Complete Genomics, Inc.
Toll-free: (855) 267-5358 | Direct: (650) 943-2651
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