Sequence analysis Toolkit

Build

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.

TrimPipe

trimpipe.zip
Author: Jonathan Cummings
Last Revision: 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.zip
Author: Jonathan Cummings
Last Revision: Apr 2013
Description: Runhist - Given the input directory, output histogram plots to the output directory in pdf form.

MRPlot

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.

MCLSyntenyPlotting

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.

LatticeHist

latticehist.zip
Author: Jonathan Cummings
Last Revision: Apr 2013
Description: Creates a lattice of histograms using data from a specific csv file.

TaxonomySearch

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.

Combiner

combiner.zip
Author: Jonathan Cummings
Last Revision: Apr 2013
Description: Given two fastq files and an output file, combine the two input files into the output file.

bioinformatics/scripts/toolkit.txt · Last modified: 2015/10/15 22:37 (external edit)
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