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Thursday, April 28, 2011

Dealing with FASTQ's

I posted some code for dealing with FASTq's. They're all written in C++, and each one replaces a tool that's between 3 and 50 times slower. The scoring metric they use for "anchored sequence alignment" has been improved. Also, they contain lots of "do what I mean" features, allowing the user to focus on the results, and not on the mechanics of processing sequencing data.

The essential tasks they accomplish are sequence quality filtering, adapter/primer removal, demultiplexing and paired-end joining (stitching):

They have to be compiled, but they are each "monolithic" ... and require no libraries, headers, etc. I tested fastq-join on Linux and Windows, so I know it compiles easily. The other 2 tools have only been tested on Linux.

See: https://code.google.com/p/ea-utils/

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