Banana Slug Genomics

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====== QSRA ======

===== Overview =====
QSRA[(cite:qrsa>Douglas W Bryant Jr, Weng-Keen Wong, and Todd C Mockler. QSRA – a quality-value guided //de novo// short read assembler. //BMC Bioinformatics// 2009, 10:69, doi:[[http://dx.doi.org/10.1186/1471-2105-10-69|10.1186/1471-2105-10-69]].)] stands for **Q**uality Value Guided **S**hort **R**ead **A**ssembler.

QSRA, as the name implies, is a quality value guided //de novo// short read DNA assembler. It builds upon the VCAKE algorithm and assembles faster than VCAKE.[(cite:qrsa)]

==== Installing ====
Get the source files and compile QSRA:

<code>
cd /campusdata/BME235/programs
wget http://qsra.cgrb.oregonstate.edu/files/QSRA.tar.gz
tar xfz QSRA.tar.gz
mv QSRA.tar.gz QSRA/
cd QSRA
make
</code>

Copy the compiled binary to the /campusdata/BME235/bin directory:

<code>
cp qsra /campusdata/BME235/bin/
</code>

==== Website ====
[[http://qsra.cgrb.oregonstate.edu/]]

==== Source and Documentation ====
Source: [[http://qsra.cgrb.oregonstate.edu/files/QSRA.tar.gz]]

Documentation (README): [[http://qsra.cgrb.oregonstate.edu/files/readme.txt]]

==== Binaries ====
Linux x86 (presumably 32 bit; not yet tested): [[http://qsra.cgrb.oregonstate.edu/files/qsra]]

Note: This is a link to the binary used for the initial publication of QSRA. 4 GB minimum RAM is recommended, as per the README.

===== References =====
<refnotes>notes-separator: none</refnotes>
~~REFNOTES cite~~

Banana Slug Genomics

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