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3
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1 BACKGROUND:
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2 ClusterFAST is a tool for finding translocation in next generation sequencing data developed by Haley Abel and Eric Duncavage at Washington University in St. Louis, MO. A manuscript detailing the use of ClusterFAST ican be found at: http://www.ncbi.nlm.nih.gov/pubmed/?term=24813172. For questions or comments please email eduncavage@path.wustl.edu
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3
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4 ClusterFAST is a pipeline for highly specific detection of translocations from high-coverage targeted capture sequence data. It detects translocation breakpoints with single base accuracy and provides assembled contigs for PCR validation. ClustFAST is implemented in Java for improved interoperability and can be run from the command line via a perl script. ClusterFAST is meant for translocation detection from targeted regions and requires a picard-style interval file containing the targets (e.g., ALK_MLL.txt). Numerous output files are created during the workflow (see below) to allow for error checking. The current version of ClusterFAST uses velvet to assemble contigs during the final step, however other assemblers can be substituted.
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5
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6 GALAXY WRAPPER:
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7 This galaxy wrapper was created by Geert Vandeweyer. It represents a static snapshot of ClusterFast version 0611 (received from the authors on 2014-07-24). For questions regarding its functionality, contact me by geert.vandeweyer@uantwerpen.be
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8
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9 LICENSE AND DISCLAIMER:
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10 ClusterFAST is protected by copyright, is distributed under the GNU GPL public license, and may be used freely for research purposes. The use of ClusterFAST for the purpose of financial profit or the inclusion/distribution with for-profit software not covered by GNU public license is prohibited. Please email eduncavage@path.wustl.edu for information on commercial license. The performance of ClusterFAST will vary depending on many sequencing parameters and must be validated by individual labratories.
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11
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12 INSTALLATION:
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13 Galaxy should be able to install all depedencies automatically. These include
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14 - samtools
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15 - blat-server
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16 - velvet
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17 - novoalign
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18
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19 After installation, you need to update several environment settings for the dependencies to work correctly.
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20
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21 - NOVOALIGN path: (novoalign binaries are NOT automatically installed, see package_novoalign for details ) : <tool_dependency_dir>/environment_settings/NOVOALIGN_PATH/geert-vandeweyer/package_novoalign/<hash_string>/env.sh
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22 - index files (clusterfast.loc holds info on 2bit/fasta/novoalign references) : <path>/galaxy-dist/tool-data/<toolshed>/repos/geert-vandeweyer/clusterfast/<hash>/clusterfast.loc. Read comments for the exact syntax.
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23 - number of velvet threads : <tool_dependency_dir>/environment_settings/OMP_THREAD_LIMIT/geert-vandeweyer/package_velvet/<hash_string>/env.sh
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24
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25
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