Re: SolexaQA 2.2 HiSeq2500 data

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MPC

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May 28, 2013, 4:46:00 PM5/28/13

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SolexaQA does not presently support compressed files. Try decompressing the file and then running SolexaQA.

It is perhaps worth briefly noting the philosophy behind this decision. Currently the SolexaQA package is written entirely in standard Perl. The software can be run as is on any machine with Perl installed -- which includes nearly all Linux and OS X systems by default, and any Windows machine with active Perl. As far as we are aware, modifying SolexaQA to support compressed files would complicate the software installation process by requiring users to install non-standard Perl packages from CPAN. As experienced Perl users know, installing packages from CPAN can sometimes be challenging. In our experience, users with limited Perl experience struggle with this (and often just give up entirely). Therefore, we have erred on the side of providing an extremely easy installation process for SolexaQA -- at the price of not supporting compressed files.

If there are other solutions to this issue, the code maintainers would be pleased to hear them.