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MANIFEST
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code-of-conduct.md
config.bak/emails.conf
config.bak/plugins.conf
config.bak/README.md
config.bak/settings.conf
config.bak/taxonProperties.conf
CONTRIBUTING.md
db/wgMLST/.dummy
DISCLAIMER.md
docs/images/overview.png
docs/INSTALL.advanced.md
docs/INSTALL.md
docs/plugins/addReadMetrics.pl.md
docs/plugins/assembleAll.pl.md
docs/plugins/baseBalance.pl.md
docs/PLUGINSDEV.md
docs/plugins/emailWhoever.pl.md
docs/plugins/guessTaxon.pl.md
docs/PLUGINS.md
docs/plugins/README.md
docs/plugins/sn_crypto_assembleAll.pl.md
docs/plugins/sn_crypto_gp60.pl.md
docs/plugins/sn_detectContamination-kraken.pl.md
docs/plugins/sn_detectContamination-mlst.pl.md
docs/plugins/sn_detectContamination.pl.md
docs/plugins/sn_helloWorld.pl.md
docs/plugins/sn_helloWorld.py.md
docs/plugins/sn_helloWorld.sh.md
docs/plugins/sn_immediateStatus.pl.md
docs/plugins/sn_iontorrent_assembleAll.pl.md
docs/plugins/sn_iontorrent_parseSampleSheet.pl.md
docs/plugins/sn_mlst.pl.md
docs/plugins/sn_mlst-wg.pl.md
docs/plugins/sn_parseSampleSheet.pl.md
docs/plugins/sn_passfail.pl.md
docs/plugins/sn_report.pl.md
docs/plugins/sn_SalmID.pl.md
docs/plugins/sn_saveFailedGenomes.pl.md
docs/plugins/sn_staramr.pl.md
docs/plugins/transferFilesToRemoteComputers.pl.md
docs/SneakerNetInput.md
example/images/MiSeqSampleEditSheet.jpg
example/images/saveAs.jpg
example/images/warning1.jpg
example/images/warning2.jpg
example/inbox/test-15-001/A_1.fastq.gz
example/inbox/test-15-001/A_2.fastq.gz
example/inbox/test-15-001/B_1.fastq.gz
example/inbox/test-15-001/B_2.fastq.gz
example/inbox/test-15-001/config.xml
example/inbox/test-15-001/QC/CompletedJobInfo.xml
example/inbox/test-15-001/QC/GenerateFASTQRunStatistics.xml
example/inbox/test-15-001/QC/InterOp/CorrectedIntMetricsOut.bin
example/inbox/test-15-001/QC/RunInfo.xml
example/inbox/test-15-001/QC/runParameters.xml
example/inbox/test-15-001/readMetrics.tsv
example/inbox/test-15-001/SampleSheet.csv
example/M00123-18-001-test/SneakerNet/forEmail/report.html
example/README.md
example/Rover_NexteraXTv2_16samples.xlsx
example/Rover_NexteraXTv2_48samples.xlsx
.gitignore
.github/ISSUE_TEMPLATE/bug_report.md
.github/ISSUE_TEMPLATE/feature_request.md
.github/ISSUE_TEMPLATE/plugin-contribution.md
lib/perl5/SneakerNet.pm
LICENSE
Makefile.PL
MANIFEST This list of files
paper/paper.bib
paper/paper.md
README.md
scripts/SneakerNet.ionTorrent.ro.pl
scripts/SneakerNet.pl
scripts/SneakerNetPlugins.pl
scripts/SneakerNet.roRun.pl
SneakerNet.plugins/addReadMetrics.pl
SneakerNet.plugins/assembleAll.pl
SneakerNet.plugins/baseBalance.pl
SneakerNet.plugins/emailWhoever.pl
SneakerNet.plugins/read_length_quality_stats_fastq.py
SneakerNet.plugins/README.md
SneakerNet.plugins/sn_crypto_assembleAll.pl
SneakerNet.plugins/sn_crypto_gp60.pl
SneakerNet.plugins/sn_detectContamination-kraken.pl
SneakerNet.plugins/sn_detectContamination-mlst.pl
SneakerNet.plugins/sn_detectContamination.pl
SneakerNet.plugins/sn_helloWorld.pl
SneakerNet.plugins/sn_helloWorld.py
SneakerNet.plugins/sn_helloWorld.sh
SneakerNet.plugins/sn_immediateStatus.pl
SneakerNet.plugins/sn_iontorrent_assembleAll.pl
SneakerNet.plugins/sn_mlst.pl
SneakerNet.plugins/sn_mlst-wg.pl
SneakerNet.plugins/sn_parseSampleSheet.pl
SneakerNet.plugins/sn_passfail.pl
SneakerNet.plugins/sn_report.pl
SneakerNet.plugins/sn_saveFailedGenomes.pl
SneakerNet.plugins/sn_staramr.pl
SneakerNet.plugins/transferFilesToRemoteComputers.pl
t/00_env.t
t/01_sn_parseSampleSheet.t
t/02_addReadMetrics.t
t/03_assembleAll.t
t/05_kraken.t
t/06_baseBalance.t
t/07_sn_passfail.t
t/08_transferFilesToRemoteComputers.t
t/09_emailWhoever.t
t/40_metagenomics.t
t/90_universalOptionsInPlugins.t
t/91_pluginsDocumentation.t
t/M00123-18-001-test/2010EL-1786_1.fastq.gz
t/M00123-18-001-test/2010EL-1786_2.fastq.gz
t/M00123-18-001-test/2010EL-1786.fasta.gz
t/M00123-18-001-test/FA1090_1.fastq.gz
t/M00123-18-001-test/FA1090_2.fastq.gz
t/M00123-18-001-test/FA1090.fasta.gz
t/M00123-18-001-test/Philadelphia_CDC_1.fastq.gz
t/M00123-18-001-test/Philadelphia_CDC_2.fastq.gz
t/M00123-18-001-test/Philadelphia_CDC.fasta.gz
t/M00123-18-001-test/SampleSheet.csv