Difference between revisions of "FCP"
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__NOTOC__ | __NOTOC__ | ||
| − | The fragment classification package (FCP) provides the following classifiers for assigning | + | The fragment classification package (FCP) provides the following classifiers for assigning a taxonomic attribution to metagenomic fragments or assembled scaffolds: |
| − | *Naive Bayes (NB): a composition-based, rank-specific classifier | + | *''Naive Bayes (NB)'': a composition-based, rank-specific classifier |
| − | *BLASTN: a homology-based, rank-specific classifier | + | *''BLASTN'': a homology-based, rank-specific classifier |
| − | *NB-BL: a hybrid, rank-specific classifier combining NB and BLASTN | + | *''NB-BL'': a hybrid, rank-specific classifier combining NB and BLASTN |
| − | *Epsilon-NB | + | *''Epsilon-NB'': a composition-based, rank-flexible classifier |
| − | *Lowest common ancestor (LCA): a homology-based, rank-flexible classifier | + | *''Lowest common ancestor (LCA)'': a homology-based, rank-flexible classifier |
| − | *LCA + epsilon-NB: a hybrid, rank-flexible classifier combining LCA and epsilon-NB | + | *''LCA + epsilon-NB'': a hybrid, rank-flexible classifier combining LCA and epsilon-NB |
== License == | == License == | ||
| Line 14: | Line 14: | ||
== Obtaining the Software == | == Obtaining the Software == | ||
| − | + | * [https://github.com/dparks1134/FragmentClassificationPackage/releases/download/v1.0.7/FCP_1_0_7.zip Fragment classification package v1.0.7] | |
| + | * [https://github.com/dparks1134/FragmentClassificationPackage Source code on GitHub] | ||
| + | * [[Older versions of FCP|Older versions]] | ||
| − | + | After downloading, uncompress the file and follow the installation instruction in the README.md file. Under OSX or Linux, the zip file can be uncompressed by typing <tt>unzip FCP_1_0_7.zip</tt> at the command prompt. Under Windows 7, the zip file can be uncompressed by right-clicking on the file and selecting 'Extract all...' from the popup menu. The FCP has been tested under OS X Snow Leopard, Linux, and Windows 7. To install the FCP under OS X, gcc must be installed which is available as part of the [http://developer.apple.com/technologies/tools/ Mac Developer Tools]. | |
| − | |||
| − | + | == Citing the FCP == | |
| − | + | If you find this software helpful in your research, please cite: | |
| − | * | + | * '''Parks, D.H., MacDonald, N.J., and Beiko, R.G. (2011). Classifying short genomic fragments from novel lineages using composition and homology. ''BMC Bioinformatics'', 12:328. ([http://www.biomedcentral.com/1471-2105/12/328 Abstract])''' |
== Contact Information == | == Contact Information == | ||
| Line 29: | Line 30: | ||
The FCP is in active development and we are interested in discussing all potential applications of this software. We encourage you to send us suggestions for new features. Suggestions, comments, and bug reports can be sent to Rob Beiko (beiko [at] cs.dal.ca). If reporting a bug, please provide as much information as possible and a simplified version of the data set which causes the bug. This will allow us to quickly resolve the issue. | The FCP is in active development and we are interested in discussing all potential applications of this software. We encourage you to send us suggestions for new features. Suggestions, comments, and bug reports can be sent to Rob Beiko (beiko [at] cs.dal.ca). If reporting a bug, please provide as much information as possible and a simplified version of the data set which causes the bug. This will allow us to quickly resolve the issue. | ||
| − | == | + | == Version History == |
| + | |||
| + | ''v1.0.7 (July 12, 2015)'' | ||
| + | * fixed AddModel.py should it accepts the desired n-mer size of new models | ||
| + | |||
| + | ''v1.0.6 (August 12, 2014)'' | ||
| + | * fixed bug with NB-BL.py which caused it to have an output format incompatible with the rest of the FCP suite | ||
| + | |||
| + | ''v1.0.5 (May 30, 2014)'' | ||
| + | * changed default k-mer size from 10 to 8 in response to the rapidly expanding number of reference genomes | ||
| + | * minor code improvements | ||
| + | |||
| + | ''v1.0.4 (April 13, 2013)'' | ||
| + | * removed need for taxonomy file from nb-train | ||
| + | * improved error reporting for nb-train and nb-classify | ||
| + | * added example illustrating use of the naive Bayes classifier independent of the FCP framework | ||
| + | |||
| + | ''v1.0.3 (July 13, 2011)'' | ||
| + | * changed NB_install.py to FCP_install.py | ||
| + | * added -protein flag to FCP_install.py to all FCP to be used with [http://kiwi.cs.dal.ca/Software/RITA RITA] | ||
| + | |||
| + | ''v1.0.2 (June 3, 2011)'' | ||
| + | * improved robustness of NB_install.py script | ||
| + | * TaxonomicSummary.py now reports both raw and normalized percentages | ||
| + | * removed need for temporary directories when running nb-classify | ||
| + | * fixed major bug in LCA+Epsilon-NB.py which was causing the epsilon parameter to be handled incorrectly | ||
| + | * fixed minor bug in LCA.py where unclassified fragments where reported as 'u' instead of 'unclassified' | ||
| − | + | ''v1.0.1 (Apr. 28, 2011)'' | |
| + | * revision to NB_install.py to account for genomes without NCBI taxonomy information | ||
| − | '' | + | ''v1.0.0 (Jan. 4, 2011)'' |
| + | * initial software release. | ||
== Funding == | == Funding == | ||
| − | The development | + | The development of this software has been supported by several organizations: |
* [http://www.killamtrusts.ca/ Killam Trusts] | * [http://www.killamtrusts.ca/ Killam Trusts] | ||
Latest revision as of 00:18, 12 July 2015
The fragment classification package (FCP) provides the following classifiers for assigning a taxonomic attribution to metagenomic fragments or assembled scaffolds:
- Naive Bayes (NB): a composition-based, rank-specific classifier
- BLASTN: a homology-based, rank-specific classifier
- NB-BL: a hybrid, rank-specific classifier combining NB and BLASTN
- Epsilon-NB: a composition-based, rank-flexible classifier
- Lowest common ancestor (LCA): a homology-based, rank-flexible classifier
- LCA + epsilon-NB: a hybrid, rank-flexible classifier combining LCA and epsilon-NB
License
This software is released under the GNU General Public License v3.0.
Obtaining the Software
After downloading, uncompress the file and follow the installation instruction in the README.md file. Under OSX or Linux, the zip file can be uncompressed by typing unzip FCP_1_0_7.zip at the command prompt. Under Windows 7, the zip file can be uncompressed by right-clicking on the file and selecting 'Extract all...' from the popup menu. The FCP has been tested under OS X Snow Leopard, Linux, and Windows 7. To install the FCP under OS X, gcc must be installed which is available as part of the Mac Developer Tools.
Citing the FCP
If you find this software helpful in your research, please cite:
- Parks, D.H., MacDonald, N.J., and Beiko, R.G. (2011). Classifying short genomic fragments from novel lineages using composition and homology. BMC Bioinformatics, 12:328. (Abstract)
Contact Information
The FCP is in active development and we are interested in discussing all potential applications of this software. We encourage you to send us suggestions for new features. Suggestions, comments, and bug reports can be sent to Rob Beiko (beiko [at] cs.dal.ca). If reporting a bug, please provide as much information as possible and a simplified version of the data set which causes the bug. This will allow us to quickly resolve the issue.
Version History
v1.0.7 (July 12, 2015)
- fixed AddModel.py should it accepts the desired n-mer size of new models
v1.0.6 (August 12, 2014)
- fixed bug with NB-BL.py which caused it to have an output format incompatible with the rest of the FCP suite
v1.0.5 (May 30, 2014)
- changed default k-mer size from 10 to 8 in response to the rapidly expanding number of reference genomes
- minor code improvements
v1.0.4 (April 13, 2013)
- removed need for taxonomy file from nb-train
- improved error reporting for nb-train and nb-classify
- added example illustrating use of the naive Bayes classifier independent of the FCP framework
v1.0.3 (July 13, 2011)
- changed NB_install.py to FCP_install.py
- added -protein flag to FCP_install.py to all FCP to be used with RITA
v1.0.2 (June 3, 2011)
- improved robustness of NB_install.py script
- TaxonomicSummary.py now reports both raw and normalized percentages
- removed need for temporary directories when running nb-classify
- fixed major bug in LCA+Epsilon-NB.py which was causing the epsilon parameter to be handled incorrectly
- fixed minor bug in LCA.py where unclassified fragments where reported as 'u' instead of 'unclassified'
v1.0.1 (Apr. 28, 2011)
- revision to NB_install.py to account for genomes without NCBI taxonomy information
v1.0.0 (Jan. 4, 2011)
- initial software release.
Funding
The development of this software has been supported by several organizations:
- Killam Trusts
- Genome Atlantic
- The Dalhousie Centre for Comparative Genomics and Evolutionary Bioinformatics, and the Tula Foundation
- The Dalhousie Faculty of Computer Science
