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Java Archives - Omixon | NGS for HLA

Java

Workflow Wednesdays – Alignments – Format conversion

04/09/2013

I could go on forever and ever about different short read aligners, but I think you get the gist of it. So let’s talk about alignment files! Most modern reference based aligners produce their output in sam format. If you’re not familiar with this file format, check out my post...

Workflow Wednesdays – Short read aligners – Omixon Variant Toolkit

28/08/2013

Omixon Variant Toolkit (aka Omixon Read Mapper or ORM)is our “own” alignment algorithm which is available as a standalone java application or in Omixon Target. The aligner actually contains two, slightly different algorithms*: one for shorter Illumina reads, called “bridge” and one for longer (IonTorrent and 454) reads, called “lace”....