| This Release | Bio-Tradis-1.132140 | [Download] [Browse] | 02 Aug 2013 | |||
| Latest Release | Bio-Tradis-1.132190 | [Download] [Browse] | 07 Aug 2013 | |||
| Links | [ Discussion Forum ] [ View/Report Bugs ] [ Website ] [ Dependencies ] [ Other Tools ] | |||||
| Repository | https://github.com/sanger-pathogens/Bio-Tradis.git | |||||
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| License | The GNU General Public License, Version not specified | |||||
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| 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 | Add tags to the start of the sequences | ||
| 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 |
| 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 |
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README.md |
