Jun 22th 2009
e-GenoType version (0.96) released [Changelog].

May 29th 2009
e-GenoType version (0.94) released [Changelog].

May 19th 2009
First version of e-GenoType released (0.93) [Changelog].

What is e-GenoType?

Processing large volumes of short reads from second generation sequencing instruments is computationally costly and time consuming. Usually the first step of this process requires mapping to align the sequence reads back to the reference. This is often the most costly step as mapping algorithms are computationally intensive and require a fair amount of CPU, memory and storage. It is not uncommon for days to pass before basic information such as mappable yield is available, and it takes even longer to generate SNP calls and genotype information. To serve the need for rapid analysis of second generation sequence data we have developed e-GenoType, a set of tools aimed at rapidly screening sequence data for known alleles that can generate genotype data in minutes or hours instead of days or weeks.

As it is a known allele screening method, e-GenoType cannot do de novo variation discovery, but as community efforts such as the thousand genomes project progress, the known allele databases with dramatically increase in size. In short, this will never replace a full mapping and variation calling analysis of a whole genome sample, but it is an increasingly useful Supplement as the universe of known human variation rapidly expands.

How to get started

Check the README that comes with the distribution.

This plot displays the egcs-counter output when run against one of our ABi SOLiD runs. Each square is colored based on the base 10 log of the number of probed SNP sites observed with the given number of reference and variant alleles.

Questions? Comments?

Great! feel free to email us at:

Last modified: Thursday, 17-Feb-2011 12:15:03 CST