Andrew Page > Bio-Tradis

Bio-Tradis

This Release Bio-Tradis-1.3.0  [Download] [Browse 13 Apr 2016
Other Releases
Links Discussion Forum ] [ View/Report Bugs (1) ] [ Website ] [ Dependencies ] [ Other Tools ]
Repository https://github.com/sanger-pathogens/Bio-Tradis.git
CPAN Testers FAIL (90)   [ View Reports ] [ Perl/Platform Version Matrix ]
Rating      (0 Reviews) [ Rate this distribution ]
License The GNU General Public License, Version not specified
Special Files
AUTHORS
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     1.3.0
Bio::Tradis::AddTagsToSeq Takes a BAM file and creates a new BAM with tr and tq tags added to the sequence and quality strings.     1.3.0
Bio::Tradis::Analysis::Exceptions Custom exceptions     1.3.0
Bio::Tradis::Analysis::InsertSite Take in a bam file and plot the start position of each read     1.3.0
Bio::Tradis::CombinePlots Combine multiple plotfiles and generate updated statistics for the combined files     1.3.0
Bio::Tradis::CommandLine::AddTags Add given tags to the start of the sequence     1.3.0
Bio::Tradis::CommandLine::CheckTags Check for presence of tr tag in BAM file     1.3.0
Bio::Tradis::CommandLine::FilterFastqTags Remove given tags from the start of the sequence     1.3.0
Bio::Tradis::CommandLine::PlotCombine Combine multiple plotfiles and generate updated statistics for the combined files     1.3.0
Bio::Tradis::CommandLine::PlotTradis Generate plots as part of a tradis analysis     1.3.0
Bio::Tradis::CommandLine::RemoveFastqTags Remove given tags from the start of the sequence     1.3.0
Bio::Tradis::CommandLine::RunMapping Perform mapping     1.3.0
Bio::Tradis::CommandLine::TradisAnalysis Perform full tradis analysis     1.3.0
Bio::Tradis::CommandLine::TradisBam Adds tags to sequences if tags are present     1.3.0
Bio::Tradis::DetectTags Detect tr tags in BAM file     1.3.0
Bio::Tradis::Exception Exceptions for input data     1.3.0
Bio::Tradis::FilterTags Filter tags in a fastq file     1.3.0
Bio::Tradis::Map Perform mapping     1.3.0
Bio::Tradis::Parser::Bam Very basic BAM parser. Limited functionality.     1.3.0
Bio::Tradis::Parser::Cigar Take in a cigar string and output start and end relative to the reference sequence     1.3.0
Bio::Tradis::Parser::Fastq Basic FastQ parser.     1.3.0
Bio::Tradis::RemoveTags Remove tags from seqs a fastq file     1.3.0
Bio::Tradis::RunTradis Perform all steps required for a tradis analysis     1.3.0
Bio::Tradis::Samtools Change samtools syntax depending on version found     1.3.0
Bio::Tradis::TradisPlot Generate plots as part of a tradis analysis     1.3.0

Documentation

check_tags check if tr tag is present  
combine_tradis_plot Combine multiple plotfiles and generate updated statistics for the combined files  
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_comparison.R tradis_comparison.R  
tradis_essentiality.R tradis_essentiality.R  
tradis_gene_insert_sites Generate insertion site details from TraDIS pipeline plots  
tradis_merge_plots  
tradis_plot Generate plots as part of a tradis analysis  

Other Files

README.md