Files

• AUTHORS
• BioTraDISTutorial.pdf
• CHANGELOG.md
• Dockerfile
• LICENSE
• MANIFEST
• META.json
• META.yml
• Makefile.PL
• README
• README.md
• _config.yml
• bcinstall.log
• bin/add_tradis_tags
• bin/bacteria_tradis
• bin/check_tradis_tags
• bin/combine_tradis_plots
• bin/filter_tradis_tags
• bin/remove_tradis_tags
• bin/tradis_comparison.R
• bin/tradis_essentiality.R
• bin/tradis_gene_insert_sites
• bin/tradis_merge_plots
• bin/tradis_plot
• build/bwa-0.7.17.tbz
• build/samtools-1.3.tbz
• build/smalt-0.7.6.tgz
• build/tabix-master.tgz
• dist.ini
• install_dependencies.sh
• lib/Bio/Tradis.pm
• lib/Bio/Tradis/AddTagsToSeq.pm
• lib/Bio/Tradis/Analysis/Exceptions.pm
• lib/Bio/Tradis/Analysis/InsertSite.pm
• lib/Bio/Tradis/CombinePlots.pm
• lib/Bio/Tradis/CommandLine/AddTags.pm
• lib/Bio/Tradis/CommandLine/CheckTags.pm
• lib/Bio/Tradis/CommandLine/FilterFastqTags.pm
• lib/Bio/Tradis/CommandLine/PlotCombine.pm
• lib/Bio/Tradis/CommandLine/PlotTradis.pm
• lib/Bio/Tradis/CommandLine/RemoveFastqTags.pm
• lib/Bio/Tradis/CommandLine/RunMapping.pm
• lib/Bio/Tradis/CommandLine/TradisAnalysis.pm
• lib/Bio/Tradis/CommandLine/TradisBam.pm
• lib/Bio/Tradis/DetectTags.pm
• lib/Bio/Tradis/Exception.pm
• lib/Bio/Tradis/FilterTags.pm
• lib/Bio/Tradis/Map.pm
• lib/Bio/Tradis/Parser/Bam.pm
• lib/Bio/Tradis/Parser/Cigar.pm
• lib/Bio/Tradis/Parser/Fastq.pm
• lib/Bio/Tradis/RemoveTags.pm
• lib/Bio/Tradis/RunTradis.pm
• lib/Bio/Tradis/Samtools.pm
• lib/Bio/Tradis/TradisPlot.pm
• recipes/Tradis_SR_RR_12dark_42r1_rehyb12_index8.xml
• recipes/Tradis_adapter_primers.xlsx
• recipes/Transposon10/Chemistry/Chemistry.xml
• recipes/Transposon10/Exposures/Sony.xml
• recipes/Transposon10/Exposures/SonyV2.xml
• recipes/Transposon10/Protocol/1Read1Index.xml
• recipes/Transposon10/Protocol/1Read2Index.xml
• recipes/Transposon10/Protocol/2Read1Index.xml
• recipes/Transposon10/Protocol/2Read2Index.xml
• recipes/Transposon10/Reads/Reads.xml
• recipes/Transposon10/Reagents/MaintenanceWash.xml
• recipes/Transposon10/Reagents/PostRunWash.xml
• recipes/Transposon10/Reagents/Sequencing.xml
• recipes/Transposon10/Wash/LineWash.xml
• recipes/Transposon10/Wash/MaintenanceWash.xml
• recipes/Transposon10/Wash/PostRunWash.xml
• recipes/Transposon10/Wash/PostRunWashOriginal.xml
• recipes/Transposon10/Wash/StandbyWash.xml
• recipes/Transposon12/Chemistry/Chemistry.xml
• recipes/Transposon12/Exposures/Sony.xml
• recipes/Transposon12/Exposures/SonyV2.xml
• recipes/Transposon12/Protocol/1Read1Index.xml
• recipes/Transposon12/Protocol/1Read2Index.xml
• recipes/Transposon12/Protocol/2Read1Index.xml
• recipes/Transposon12/Protocol/2Read2Index.xml
• recipes/Transposon12/Reads/Reads.xml
• recipes/Transposon12/Reagents/MaintenanceWash.xml
• recipes/Transposon12/Reagents/PostRunWash.xml
• recipes/Transposon12/Reagents/Sequencing.xml
• recipes/Transposon12/Wash/130702_ImplementingCarryoverDecontamWash_v3.docx
• recipes/Transposon12/Wash/LineWash.xml
• recipes/Transposon12/Wash/MaintenanceWash.xml
• recipes/Transposon12/Wash/PostRunWash.xml
• recipes/Transposon12/Wash/PostRunWashOriginal.xml
• recipes/Transposon12/Wash/StandbyWash.xml
• software_license
• source_path
• t/00-report-prereqs.dd
• t/00-report-prereqs.t
• t/Bio/Tradis/AddTagsToSeq.t
• t/Bio/Tradis/Analysis/InsertSite.t
• t/Bio/Tradis/CombinePlots.t
• t/Bio/Tradis/CommandLine/TradisAnalysis.t
• t/Bio/Tradis/DetectTags.t
• t/Bio/Tradis/FilterTags.t
• t/Bio/Tradis/Map.t
• t/Bio/Tradis/Parser/Bam.t
• t/Bio/Tradis/Parser/Cigar.t
• t/Bio/Tradis/Parser/Fastq.t
• t/Bio/Tradis/RemoveTags.t
• t/Bio/Tradis/RunTradisBWA.t
• t/Bio/Tradis/RunTradisSmalt.t
• t/Bio/Tradis/RunTradisTaglessBwa.t
• t/Bio/Tradis/RunTradisTaglessSmalt.t
• t/Bio/Tradis/TradisPlot.t
• t/data/AddTags/expected_tradis.bam
• t/data/AddTags/expected_tradis.cram
• t/data/AddTags/sample_sm_no_tr.bam
• t/data/AddTags/sample_sm_tr.bam
• t/data/AddTags/sample_sm_tr.cram
• t/data/CombinePlots/comb_expected.stats
• t/data/CombinePlots/comb_sample.txt
• t/data/CombinePlots/first.expected.plot
• t/data/CombinePlots/sample1.sm.plot.gz
• t/data/CombinePlots/sample2.sm.plot.gz
• t/data/CombinePlots/second.expected.plot
• t/data/CombinePlots/tabix_sorted.insert_site_plot.gz
• t/data/CombinePlots/tabix_sorted.insert_site_plot.gz.tbi
• t/data/CombinePlots/test1.plot
• t/data/CombinePlots/test2.plot
• t/data/CombinePlots/test3.plot
• t/data/CombinePlots/test4.plot
• t/data/CombinePlots/zip_comb_exp.plot
• t/data/CombinePlots/zip_comb_exp.stats
• t/data/CombinePlots/zip_comb_list.txt
• t/data/CommandLine/fastq.list
• t/data/CommandLine/test_1.fastq
• t/data/CommandLine/test_2.fastq
• t/data/DetectTags/AE004091.fasta
• t/data/DetectTags/AE004091.fasta.fai
• t/data/DetectTags/sample_sm_no_tr.bam
• t/data/DetectTags/sample_sm_tr.bam
• t/data/DetectTags/sample_sm_tr.cram
• t/data/FilterTags/expected.1mm.caa.fastq
• t/data/FilterTags/expected.caa.fastq
• t/data/FilterTags/expected.tna.fastq
• t/data/FilterTags/sample.fastq
• t/data/FilterTags/sample.fastq.gz
• t/data/InsertSite/2_reads.bam
• t/data/InsertSite/small_multi_sequence.bam
• t/data/Map/expected.bwa.mapped
• t/data/Map/expected.smalt.mapped
• t/data/Map/smallref.fa
• t/data/Map/test.fastq
• t/data/Parsers/test.bam
• t/data/Parsers/test.fastq
• t/data/RemoveTags/expected.rm.1mm.caa.fastq
• t/data/RemoveTags/expected.rm.caa.fastq
• t/data/RemoveTags/expected.rm.tna.fastq
• t/data/RemoveTags/sample.caa.fastq
• t/data/RemoveTags/sample.tna.fastq
• t/data/RunTradisBWA/expected.1mm.plot.gz
• t/data/RunTradisBWA/expected.plot.gz
• t/data/RunTradisBWA/filelist.txt
• t/data/RunTradisBWA/filtered.fastq
• t/data/RunTradisBWA/mapped.sam
• t/data/RunTradisBWA/notags.fastq
• t/data/RunTradisBWA/smallref.fa
• t/data/RunTradisBWA/test.tagged.fastq
• t/data/RunTradisBWA/test.tagged.fastq.gz
• t/data/RunTradisBWA/test2.tagged.fastq
• t/data/RunTradisBWA/test2.tagged.fastq.gz
• t/data/RunTradisSmalt/expected.1mm.plot.gz
• t/data/RunTradisSmalt/expected.plot.gz
• t/data/RunTradisSmalt/filelist.txt
• t/data/RunTradisSmalt/filtered.fastq
• t/data/RunTradisSmalt/mapped.sam
• t/data/RunTradisSmalt/notags.fastq
• t/data/RunTradisSmalt/smallref.fa
• t/data/RunTradisSmalt/test.tagged.fastq
• t/data/RunTradisSmalt/test.tagged.fastq.gz
• t/data/RunTradisSmalt/test2.tagged.fastq
• t/data/RunTradisSmalt/test2.tagged.fastq.gz
• t/data/RunTradisTaglessBWA/expected.plot.gz
• t/data/RunTradisTaglessBWA/filelist.txt
• t/data/RunTradisTaglessBWA/mapped.sam
• t/data/RunTradisTaglessBWA/notags.fastq
• t/data/RunTradisTaglessBWA/smallref.fa
• t/data/RunTradisTaglessSmalt/expected.plot.gz
• t/data/RunTradisTaglessSmalt/mapped.sam
• t/data/RunTradisTaglessSmalt/notags.fastq
• t/data/RunTradisTaglessSmalt/smallref.fa
• t/data/TradisPlot/expected.plot.gz
• t/data/TradisPlot/sample.fastq
• t/data/TradisPlot/test.mapped.bam
• t/requires_external.t
• xt/author/00-compile.t
• xt/author/pod-syntax.t