Carla Cummins > Bio-Tradis

Bio-Tradis

This Release Bio-Tradis-1.132190  [Download] [Browse 07 Aug 2013
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Repository https://github.com/sanger-pathogens/Bio-Tradis.git
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License The GNU General Public License, Version not specified
Special Files
LICENSE
Makefile.PL
MANIFEST
META.yml
README

Modules

Bio::Tradis Bio-Tradis contains a set of tools to analyse the output from TraDIS analyses. For more information on the TraDIS method, see http://genome.cshlp.org/content/19/12/2308      
Bio::Tradis::AddTagsToSeq Takes a BAM file and creates a new BAM with tr and tq tags added to the sequence and quality strings.      
Bio::Tradis::Analysis::Exceptions      
Bio::Tradis::Analysis::InsertSite      
Bio::Tradis::CommandLine::AddTags Add given tags to the start of the sequence      
Bio::Tradis::CommandLine::CheckTags Check for presence of tr tag in BAM file      
Bio::Tradis::CommandLine::FilterFastqTags Remove given tags from the start of the sequence      
Bio::Tradis::CommandLine::PlotTradis Generate plots as part of a tradis analysis      
Bio::Tradis::CommandLine::RemoveFastqTags Remove given tags from the start of the sequence      
Bio::Tradis::CommandLine::RunMapping Perform mapping      
Bio::Tradis::CommandLine::TradisAnalysis Perform full tradis analysis      
Bio::Tradis::CommandLine::TradisBam Adds tags to sequences if tags are present      
Bio::Tradis::DetectTags Detect tr tags in BAM file      
Bio::Tradis::FilterTags Filter tags in a fastq file      
Bio::Tradis::Map Perform mapping      
Bio::Tradis::Parser::Bam Very basic BAM parser. Limited functionality.      
Bio::Tradis::Parser::Fastq Basic FastQ parser.      
Bio::Tradis::RemoveTags Remove tags from seqs a fastq file      
Bio::Tradis::RunTradis Perform all steps required for a tradis analysis      
Bio::Tradis::TradisPlot Generate plots as part of a tradis analysis      

Documentation

check_tags check if tr tag is present  
filter_tags filter tags at start of fastq sequences  
remove_tags remove user specified tags from start of fastq sequences  
run_tradis Perform full tradis analysis  
tradis_plot Generate plots as part of a tradis analysis  

Other Files

README.md