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# This file was automatically generated by Dist::Zilla::Plugin::Manifest v6.012.
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