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1 BWA-MEM wrapper
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2 ===============
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3
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4 This is a wrapper for BWA_, a software package for mapping low-divergent sequences against a large reference genome. This wrapper supports only the latest algorithm, BWA-MEM, which is generally recommended for high-quality queries as it is faster and more accurate. BWA-MEM also has better performance than BWA-backtrack for 70-100bp Illumina reads.
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5
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6 .. _BWA: http://bio-bwa.sourceforge.net/
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7
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8 If you need a wrapper for the old BWA-backtrack algorithm, you may install http://toolshed.g2.bx.psu.edu/view/devteam/bwa_wrappers repository.
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9
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10 Configuration
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11 -------------
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12
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13 bwa_mem tool may be configured to use more than one CPU core by selecting an appropriate destination for this tool in Galaxy job_conf.xml file (see https://wiki.galaxyproject.org/Admin/Config/Jobs and https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster ).
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14
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15 If you are using Galaxy release_2013.11.04 or later, this tool will automatically use the number of CPU cores allocated by the job runner according to the configuration of the destination selected for this tool.
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16
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17 If instead you are using an older Galaxy release, you should also add a line
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18
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19 GALAXY_SLOTS=N; export GALAXY_SLOTS
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20
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21 (where N is the number of CPU cores allocated by the job runner for this tool) to the file
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22
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23 <tool_dependencies_dir>/bwa/0.7.7/crs4/bwa_mem/<hash_string>/env.sh
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24
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25 Version history
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26 ---------------
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27
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28 - Release 0: Initial release in the Tool Shed. This is a fork of http://toolshed.g2.bx.psu.edu/view/yufei-luo/bwa_0_7_5 repository with the following changes: Remove .loc file, only .loc.sample should be included. Fix bwa_index.loc.sample file to contain only comments. Add suppressHeader param as in bwa_wrappers. Use $GALAXY_SLOTS environment variable when available. Add <version_command> and <help>. Remove unused import. Fix spacing and typos. Use new recommended citation. Add tool_dependencies.xml . Rename to bwa_mem. Remove definitively colorspace support. Use optparse instead of argparse since Galaxy still supports Python 2.6 .
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29
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30 Development
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31 -----------
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32
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33 Development is hosted at https://bitbucket.org/nsoranzo/bwa_mem . Contributions and bug reports are very welcome!
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