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bioinformatics:scripts:toolkit [2014/02/05 19:59] simroux [Runhist.zip] |
bioinformatics:scripts:toolkit [2015/10/15 22:37] (current) |
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===== Sequence analysis Toolkit ===== | ===== Sequence analysis Toolkit ===== | ||
==== Build ==== | ==== Build ==== | ||
+ | {{bioinformatics:scripts:build.zip}}\\ | ||
+ | **Author:** Brandon Webb, Zachary Hare, Devesh Chourasiya\\ | ||
+ | **Last Revision:** May 2013\\ | ||
+ | **Description:** Build.PL automatically installs all necessary resources and files to the user-specified directory or default directory.\\ | ||
- | === Author : === | ||
- | Brandon Webb, Zachary Hare, Devesh Chourasiya | ||
- | === Last Revision : === | ||
- | May 2013 | ||
- | === Description : === | ||
- | Build.PL automatically installs all necessary resources and files to the user-specified directory or default directory. | ||
==== TrimPipe ==== | ==== TrimPipe ==== | ||
- | {{:bioinformatics:scripts:trimpipe.zip}} | + | {{:bioinformatics:scripts:trimpipe.zip}}\\ |
- | === Author : === | + | **Author:** Jonathan Cummings\\ |
- | Jonathan Cummings | + | **Last Revision:** Apr 2013\\ |
- | === Last Revision : === | + | **Description:** TrimPipe - Given a directory with .fastq or .fastq.gz files, will trim the files with DynamicTrim.pl and then use FastQC to perform quality analysis.\\ |
- | Apr 2013 | + | |
- | === Description : === | + | |
- | TrimPipe - Given a directory with .fastq or .fastq.gz files, will trim the files with DynamicTrim.pl and then use FastQC to perform quality analysis. | + | |
==== Runhist ==== | ==== Runhist ==== | ||
- | {{:bioinformatics:scripts:runhist.zip}} | + | {{:bioinformatics:scripts:runhist.zip}}\\ |
- | === Author : === | + | **Author:** Jonathan Cummings\\ |
- | Jonathan Cummings | + | **Last Revision:** Apr 2013\\ |
- | === Last Revision : === | + | **Description:** Runhist - Given the input directory, output histogram plots to the output directory in pdf form.\\ |
- | Apr 2013 | + | |
- | === Description : === | + | |
- | Runhist - Given the input directory, output histogram plots to the output directory in pdf form. | + | |
==== MRPlot ==== | ==== MRPlot ==== | ||
+ | {{:bioinformatics:scripts:mrplot.zip}}\\ | ||
+ | **Author:** Brandon Webb\\ | ||
+ | **Last Revision:** Apr 2013\\ | ||
+ | **Description:** MRPlot - Given a BLAST or CAMERA ,csv output, parse and format an output .csv file (CAMERA dependent), recruitment plot file, and GNU plot file.\\ | ||
- | === Author : === | ||
- | Brandon Webb | ||
- | === Last Revision : === | ||
- | Apr 2013 | ||
- | === Description : === | ||
- | MRPlot - Given a BLAST or CAMERA ,csv output, parse and format an output .csv file (CAMERA dependent), recruitment plot file, and GNU plot file. | ||
==== MCLSyntenyPlotting ==== | ==== MCLSyntenyPlotting ==== | ||
+ | {{:bioinformatics:scripts:mclsyntenyplotting.zip}}\\ | ||
+ | **Author:** Brandon Webb\\ | ||
+ | **Last Revision:** Apr 2013\\ | ||
+ | **Description:** MCLSytenyPlotting -- Given a MCL output file, parse and format an synteny csv file for GNU plotting.\\ | ||
- | === Author : === | ||
- | Brandon Webb | ||
- | === Last Revision : === | ||
- | Apr 2013 | ||
- | === Description : === | ||
- | MCLSytenyPlotting -- Given a MCL output file, parse and format an synteny csv file for GNU plotting | ||
==== LatticeHist ==== | ==== LatticeHist ==== | ||
+ | {{:bioinformatics:scripts:latticehist.zip}}\\ | ||
+ | **Author:** Jonathan Cummings\\ | ||
+ | **Last Revision:** Apr 2013\\ | ||
+ | **Description:** Creates a lattice of histograms using data from a specific csv file.\\ | ||
- | === Author : === | ||
- | Jonathan Cummings | ||
- | === Last Revision : === | ||
- | Apr 2013 | ||
- | === Description : === | ||
- | Creates a lattice of histograms using data from a specific csv file. | ||
==== TaxonomySearch ==== | ==== TaxonomySearch ==== | ||
+ | {{:bioinformatics:scripts:taxonomysearch.zip}}\\ | ||
+ | **Author:** Brandon Webb\\ | ||
+ | **Last Revision:** Apr 2013\\ | ||
+ | **Description:** Given a .csv formated file containing GIvalues of each genome, query the NCBI protein database and retrieve the corresponding taxonomy name.\\ | ||
- | === Author : === | ||
- | Brandon Webb | ||
- | === Last Revision : === | ||
- | Apr 2013 | ||
- | === Description : === | ||
- | Given a .csv formated file containing GIvalues of each genome, query the NCBI protein database and retrieve the corresponding taxonomy name. | ||
==== Combiner ==== | ==== Combiner ==== | ||
- | + | {{:bioinformatics:scripts:combiner.zip}}\\ | |
- | === Author : === | + | **Author:** Jonathan Cummings\\ |
- | Jonathan Cummings | + | **Last Revision:** Apr 2013\\ |
- | === Last Revision : === | + | **Description:** Given two fastq files and an output file, combine the two input files into the output file.\\ |
- | Apr 2013 | + | |
- | === Description : === | + | |
- | Given two fastq files and an output file, combine the two input files into the output file. | + | |