├── .gitattributes ├── .github └── ISSUE_TEMPLATE │ └── bug_report.md ├── ChangeLog.txt ├── INSTALL.sh ├── LICENSE ├── README.md ├── SQLdbfile ├── edge_db.sql ├── pathogen_db.sql └── virulence_db.sql ├── ToDO ├── config_template.txt ├── deployment ├── apache2.conf ├── createDatabase.sql ├── edge_httpd.conf ├── httpd.conf ├── nmrc-deploy.sh └── public │ └── data │ └── testData ├── edge_ui ├── EDGE_input ├── EDGE_output ├── apache_conf │ ├── README │ ├── centos_httpd.conf │ ├── edge_apache.conf │ ├── edge_httpd.conf │ ├── edge_ssl.conf │ ├── pangia-vis-https.conf │ └── pangia-vis.conf ├── cgi-bin │ ├── PluploadHandler.php │ ├── batch_run_sra.pl │ ├── edge_action.cgi │ ├── edge_archive.pl │ ├── edge_auto_run.pl │ ├── edge_build_list.pl │ ├── edge_config.tmpl │ ├── edge_data_cleanup.pl │ ├── edge_db.cgi │ ├── edge_dynamic_selection.cgi │ ├── edge_dynamic_selection_ori.cgi │ ├── edge_info.cgi │ ├── edge_jobspage.cgi │ ├── edge_projects_report.cgi │ ├── edge_projectspage.cgi │ ├── edge_report.cgi │ ├── edge_sample_metadata.cgi │ ├── edge_submit.cgi │ ├── edge_um_project_monitor.pl │ ├── edge_upload.php │ ├── edge_user_management.cgi │ ├── edge_user_session.cgi │ ├── jqueryFileTree.cgi │ ├── jqueryFileTree_rel.cgi │ └── plupload_session.cgi ├── cluster │ ├── clusterSubmit.tmpl │ ├── clusterSubmit_slurm.tmpl │ └── clusterWrapper.pl ├── css │ ├── edge-output-report.css │ ├── edge-output-standalone.css │ ├── edge-output.css │ ├── edge-theme.css │ ├── edge-theme.min.css │ ├── edge.css │ ├── edge_fonts │ │ ├── .DS_Store │ │ ├── LICENSE.txt │ │ ├── OpenSans-Bold.woff2 │ │ ├── OpenSans-BoldItalic.woff2 │ │ ├── OpenSans-ExtraBold.woff2 │ │ ├── OpenSans-ExtraBoldItalic.woff2 │ │ ├── OpenSans-Italic.woff2 │ │ ├── OpenSans-Light.woff2 │ │ ├── OpenSans-LightItalic.woff2 │ │ ├── OpenSans-Semibold.woff2 │ │ ├── OpenSans-SemiboldItalic.woff2 │ │ ├── OpenSans.woff2 │ │ └── edge_fonts.css │ ├── geocomplete.css │ ├── images │ │ ├── ajax-loader.gif │ │ ├── loading.gif │ │ ├── progress.gif │ │ ├── ui-icons_444444_256x240.png │ │ └── ui-icons_555555_256x240.png │ ├── jquery-ui-datepicker.css │ ├── jquery.dataTables.custom.css │ ├── jquery.dataTables.min.css │ ├── jquery.lazyloadxt.spinner.min.css │ ├── jquery.mobile.1.4.3.min.css │ ├── jquery.mobile.datepicker.css │ ├── jquery.mobile.datepicker.theme.css │ ├── jquery.mobile.icons.min.css │ ├── jqueryFileTree.css │ ├── logo_DOE.png │ ├── spectrum.css │ ├── tooltipster.css │ ├── zocial.css │ └── zocial.svg ├── data │ ├── BatchExcelExample.xlsx │ ├── DETEQT_reference.fa │ ├── DETEQT_sample_test.txt │ ├── Host │ ├── PiReT_experimental_design.txt │ └── Ref_list.json ├── docs │ └── EDGE_ABCs.pdf ├── edgesite.installation.done ├── gpl-3.0-standalone.html ├── images │ ├── EDGE-COVID19.png │ ├── FaQCs.png │ ├── JBrowseLogo.png │ ├── NanoEDGE.png │ ├── NewToEDGE.png │ ├── PiReT.png │ ├── ProjectsReport.png │ ├── Qiime.png │ ├── bg.png │ ├── bg_blue.png │ ├── contig_edge.png │ ├── deteqt.png │ ├── directory.png │ ├── edge.ico │ ├── edge_logo.svg │ ├── edge_logo_114.png │ ├── edge_logo_192.png │ ├── edge_logo_app.png │ ├── edge_logo_icon.png │ ├── edge_logo_icon.svg │ ├── edge_logo_orig.svg │ ├── email.png │ ├── fa.png │ ├── facebookLogin.png │ ├── fasta.png │ ├── fastq.png │ ├── file.png │ ├── folder_open.png │ ├── fq.png │ ├── glyphicons-small.png │ ├── glyphicons.png │ ├── icon_running.gif │ ├── kegg_map.png │ ├── logo_DOE.png │ ├── logo_DTRA.png │ ├── logo_JSTO.png │ ├── logo_LANL.png │ ├── logo_NMRC.png │ ├── logo_NNSA.png │ ├── mission-logo.png │ ├── ncbi_sra.png │ ├── password.png │ ├── pe_orientation.png │ ├── projectlist.png │ ├── runPhame.png │ ├── sWorkflow.jpg │ ├── sWorkflow_small.jpg │ ├── sort_asc.png │ ├── sort_both.png │ ├── sort_desc.png │ ├── spinner.gif │ ├── upload.png │ ├── workflow.jpg │ ├── workflow.png │ ├── workflow_small.jpg │ └── zip.png ├── index.html ├── javascript │ ├── edge-metadata.js │ ├── edge-min.js │ ├── edge-output-standalone.js │ ├── edge-output.js │ ├── edge-projects-report.js │ ├── edge.js │ ├── edge_dynamic_selection.js │ ├── facebookJDK.js │ ├── hello.all.min.js │ ├── jquery-ui-datepicker.js │ ├── jquery.dataTables.min.js │ ├── jquery.geocomplete.js │ ├── jquery.js │ ├── jquery.lazyloadxt.autoload.min.js │ ├── jquery.lazyloadxt.extra.min.js │ ├── jquery.mobile-1.4.3.min.js │ ├── jquery.tooltipster.min.js │ ├── jqueryFileTree.js │ ├── jsphylosvg-min.js │ ├── plupload │ │ ├── Moxie.swf │ │ ├── Moxie.xap │ │ ├── i18n │ │ │ ├── ar.js │ │ │ ├── az.js │ │ │ ├── bg.js │ │ │ ├── bs.js │ │ │ ├── ca.js │ │ │ ├── cs.js │ │ │ ├── cy.js │ │ │ ├── da.js │ │ │ ├── de.js │ │ │ ├── el.js │ │ │ ├── en.js │ │ │ ├── es.js │ │ │ ├── et.js │ │ │ ├── fa.js │ │ │ ├── fi.js │ │ │ ├── fr.js │ │ │ ├── he.js │ │ │ ├── hr.js │ │ │ ├── hu.js │ │ │ ├── hy.js │ │ │ ├── id.js │ │ │ ├── it.js │ │ │ ├── ja.js │ │ │ ├── ka.js │ │ │ ├── kk.js │ │ │ ├── km.js │ │ │ ├── ko.js │ │ │ ├── ku_IQ.js │ │ │ ├── lt.js │ │ │ ├── lv.js │ │ │ ├── mn.js │ │ │ ├── ms.js │ │ │ ├── nl.js │ │ │ ├── pl.js │ │ │ ├── pt_BR.js │ │ │ ├── ro.js │ │ │ ├── ru.js │ │ │ ├── sk.js │ │ │ ├── sq.js │ │ │ ├── sr.js │ │ │ ├── sr_RS.js │ │ │ ├── sv.js │ │ │ ├── th_TH.js │ │ │ ├── tr.js │ │ │ ├── uk_UA.js │ │ │ ├── vi.js │ │ │ ├── zh_CN.js │ │ │ └── zh_TW.js │ │ ├── jquery-ui.css │ │ ├── jquery-ui.js │ │ ├── jquery-ui.min.js │ │ ├── jquery.plupload.queue │ │ │ ├── css │ │ │ │ └── jquery.plupload.queue.css │ │ │ ├── img │ │ │ │ ├── backgrounds.gif │ │ │ │ ├── buttons-disabled.png │ │ │ │ ├── buttons.png │ │ │ │ ├── delete.gif │ │ │ │ ├── done.gif │ │ │ │ ├── error.gif │ │ │ │ ├── throbber.gif │ │ │ │ └── transp50.png │ │ │ ├── jquery.plupload.queue.js │ │ │ └── jquery.plupload.queue.min.js │ │ ├── jquery.ui.plupload │ │ │ ├── css │ │ │ │ └── jquery.ui.plupload.css │ │ │ ├── img │ │ │ │ ├── loading.gif.bak │ │ │ │ └── plupload.png.bak │ │ │ ├── jquery.ui.plupload.js │ │ │ └── jquery.ui.plupload.min.js │ │ ├── moxie.js │ │ ├── moxie.min.js │ │ ├── plupload.dev.js │ │ ├── plupload.full.min.js │ │ └── plupload.min.js │ ├── raphael-min.js │ ├── social.js │ ├── spectrum.js │ └── thenBy.min.js ├── metadata_scripts │ ├── lib │ │ ├── EdgeSite.pm │ │ ├── Pathogen.pm │ │ ├── SampleMetadata.pm │ │ ├── Symptom.pm │ │ └── Travel.pm │ └── metadata_api.pl └── sys.properties.original ├── image └── logo.png ├── lib └── fastq_utility.pm ├── runPipeline ├── scripts ├── Annotation │ ├── fix_RATT_embl_feature.pl │ └── runRATT.sh ├── ClassifyBLAST.pl ├── ContigCoverageFold_plots_from_samPileup.pl ├── EDGE.desktop ├── PhaME │ ├── INSTALL.sh │ ├── README.md │ ├── lib │ │ ├── PhaME.pm │ │ └── fastq_utility.pm │ ├── phame.ctl │ ├── src │ │ ├── ParseTree.pl │ │ ├── SNP_INDEL_count.pl │ │ ├── buildSNPDB.pl │ │ ├── catAlign.pl │ │ ├── checkNUCmer.pl │ │ ├── extractGenes.pl │ │ ├── get_repeat_coords.pl │ │ ├── pal2nal.pl │ │ ├── parallel_run.pl │ │ ├── parseGapsNUCmer.pl │ │ ├── parseSitePAML.pl │ │ ├── removeGaps.pl │ │ ├── removeRepeats.pl │ │ ├── runContigNUCmer.pl │ │ ├── runHyPhy.pl │ │ ├── runNUCmer.pl │ │ ├── runPAML.pl │ │ ├── runPhaME.pl │ │ ├── runReadsMapping.pl │ │ ├── runReadsToGenome.pl │ │ ├── translate.pl │ │ └── vcfutils.pl │ └── test │ │ ├── ebola.contigs │ │ ├── phame.ctl │ │ └── ref │ │ ├── KJ660347.fasta │ │ ├── KJ660347.gff │ │ ├── ZEBOV_2002_Ilembe.fna │ │ ├── ZEBOV_2007_0Luebo.fna │ │ ├── ZEBOV_2007_1Luebo.fna │ │ ├── ZEBOV_2007_23Luebo.fna │ │ ├── ZEBOV_2007_43Luebo.fna │ │ ├── ZEBOV_2007_4Luebo.fna │ │ ├── ZEBOV_2007_5Luebo.fna │ │ └── ZEBOV_2007_9Luebo.fna ├── SNP_analysis.pl ├── SNPphy │ ├── ParseTree.pl │ ├── README.txt │ ├── SNP_INDEL_count.pl │ ├── SNPphy.ctl │ ├── SNPphy.pm │ ├── buildSNPDB.pl │ ├── checkNUCmer.pl │ ├── extractGenes.pl │ ├── fastq_utility.pm │ ├── get_repeat_coords.pl │ ├── newickToSVG.pl │ ├── pal2nal.pl │ ├── parallel_run.pl │ ├── parseGapsNUCmer.pl │ ├── parseSitePAML.pl │ ├── parse_gaps_from_nucmer_coords.pl │ ├── phylo_dot_plot.pm │ ├── removeGaps.pl │ ├── removeRepeats.pl │ ├── runContigNUCmer.pl │ ├── runNUCmer.pl │ ├── runNUCmer.pl.bak │ ├── runPAML.pl │ ├── runReadsMapping.pl │ ├── runReadsToGenome.pl │ ├── runSNPphylogeny.pl │ ├── sam2vcf.pl │ ├── samtools.pl │ ├── translate.pl │ ├── varfilter.py │ └── vcfutils.pl ├── align_trim.py ├── amplicon_coverage.py ├── bam_to_fastq.pl ├── cat_gff.pl ├── cat_multi_seq_into_one.pl ├── check_disk_cron.py ├── check_disk_usage.py ├── compare_projects │ ├── compare_projects.pl │ ├── compare_projects_html.tmpl │ └── merge_and_plot.R ├── contig_classification_plot.R ├── contig_classifier_by_bwa │ ├── class_top_hit_summary.pl │ ├── contig_classifier_by_bwa.pl │ ├── extract_fasta_by_taxa.pl │ ├── gi2lineage.pm │ ├── merge_coverage.pl │ ├── report_LCA.pl │ ├── seq_coverage.pl │ └── split_sam_by_lines.pl ├── contig_stats.pl ├── convert_bam2bigwig.pl ├── count_unmapped.pl ├── data_cleanup.pl ├── deinterleave_fastq.sh ├── download_human_refseq_genome.pl ├── edge2jbrowse_converter.pl ├── edge2jbrowse_converter_template │ ├── edge2jbrowse_converter.ctg_conf.temp │ ├── edge2jbrowse_converter.ctg_trackList_BAM.temp │ ├── edge2jbrowse_converter.ctg_trackList_PCR.temp │ ├── edge2jbrowse_converter.ref_conf.temp │ ├── edge2jbrowse_converter.ref_trackList_BAM.temp │ ├── edge2jbrowse_converter.ref_trackList_BW.temp │ ├── edge2jbrowse_converter.ref_trackList_CON.temp │ ├── edge2jbrowse_converter.ref_trackList_PCR.temp │ └── edge2jbrowse_converter.ref_trackList_VCF.temp ├── edgeWSClientProjectAdd.pl ├── edge_tools_version.pl ├── embl2genbank.pl ├── extract_fasta_from_BWA_idx.pl ├── fastacomposition.pl ├── fix_dir.sh ├── g3-from-scratch.csh ├── g3-from-scratch.csh.bak ├── g3-from-training.csh ├── g3-from-training.csh.bak ├── g3-iterated.csh ├── g3-iterated.csh.bak ├── gap_analysis.pl ├── gap_count.pl ├── genbank2embl.pl ├── genbank2fasta.pl ├── genbank2gff3.pl ├── get-motif-counts.awk ├── get_repeat_coords.pl ├── get_seqs.pl ├── glim-diff.awk ├── host_reads_removal_by_mapping.pl ├── httpserver.py ├── id_mapping_w_gi.pl ├── identify_pathogens.py ├── illumina_fastq_QC.pl ├── importBatchExcelFile.py ├── importProject.sh ├── import_project.pl ├── install_database_files.py ├── krona_portable.pl ├── match-list-col.awk ├── metadata │ ├── edge_html_metadata.tmpl │ ├── export_metadata_xlsx.pl │ └── outputMetadata_w_temp.pl ├── microbial_profiling │ ├── microbial_profiling.pl │ ├── microbial_profiling.settings.tmpl │ ├── microbial_profiling_configure.pl │ └── script │ │ ├── ImportBWA.pl │ │ ├── bam_to_fastq_by_taxa.pl │ │ ├── bwa_sam2giReadCount.pl │ │ ├── bwa_sam2read_taxa.pl │ │ ├── convert_bwa2list.pl │ │ ├── convert_bwa2metaphlan.pl │ │ ├── convert_bwa2tabTree.pl │ │ ├── convert_diamond2list.py │ │ ├── convert_diamond2megan.py │ │ ├── convert_diamond2tabTree.py │ │ ├── convert_gi2list.pl │ │ ├── convert_gi2tabTree.pl │ │ ├── convert_krakenRep2list.pl │ │ ├── convert_krakenRep2tabTree.pl │ │ ├── convert_list2radarChart.html.tmpl │ │ ├── convert_list2radarChart.pl │ │ ├── convert_list2report.pl │ │ ├── convert_list2tabTree.pl │ │ ├── convert_metaphlan2tabTree.pl │ │ ├── convert_metaphylerSrv2tabTree.pl │ │ ├── convert_metaphyler_srv2metaphlan.pl │ │ ├── convert_metascope2list.pl │ │ ├── extract_random_sequences.pl │ │ ├── fastq_info.pl │ │ ├── fastq_to_fasta_fast │ │ ├── generate_xlsx_report.pl │ │ ├── gi2lineage.pm │ │ ├── gottcha_sum_lineage.pl │ │ ├── heatmap_distinctZ_noClust_zeroRowAllow.py │ │ ├── megan_csv2pdf.pl │ │ ├── merge_list_specTaxa_by_dataset.pl │ │ ├── merge_list_specTaxa_by_tool.pl │ │ ├── mpln2krona.pl │ │ ├── mpln2list.pl │ │ ├── mpln2megan.pl │ │ ├── phylo_dot_plot.pl │ │ ├── phylo_dot_plot.pm │ │ ├── read_quantify.py │ │ ├── taxonomy.py │ │ ├── taxonomy_datatable.pl │ │ ├── uge-bwa-full.sh │ │ ├── uge-bwa.sh │ │ ├── uge-centrifuge.sh │ │ ├── uge-diamond.sh │ │ ├── uge-gottcha.sh │ │ ├── uge-gottcha2.sh │ │ ├── uge-kraken.sh │ │ ├── uge-kraken2.sh │ │ ├── uge-metaphlan.sh │ │ ├── uge-metaphlan2.sh │ │ ├── uge-metaphyler-srv.sh │ │ ├── uge-metascope.sh │ │ ├── uge-pangia.sh │ │ └── uge_helper ├── munger │ ├── edge_html_report.tmpl │ └── outputMunger_w_temp.pl ├── newickToPhyloXML.pl ├── not-acgt.awk ├── nucmer_genome_coverage.pl ├── pangia-vis-checker.sh ├── pangia_selenium_check.py ├── parse_consensus_info.pl ├── pcrAdjudication │ ├── Tm_calculate.pm │ └── pcrUniquePrimer.pl ├── pcrValidation │ ├── README │ ├── primers.fa │ ├── sequence.fasta │ └── validate_primers.pl ├── pdfPageCount.pl ├── pdfcat.pl ├── phageFinder_prepare.pl ├── plot_gff3_stats.pl ├── prepare_SNP_phylogeny.pl ├── projects_report │ ├── create_report_w_temp.pl │ ├── edge_projects_report_form.tmpl │ └── edge_projects_report_html.tmpl ├── qiime_pipeline │ ├── ChangeLog.txt │ ├── README.md │ ├── data │ ├── q2templateassets │ │ ├── css │ │ │ ├── bootstrap.min.css │ │ │ ├── normalize.css │ │ │ └── tab-parent.css │ │ ├── fonts │ │ │ ├── glyphicons-halflings-regular.eot │ │ │ ├── glyphicons-halflings-regular.svg │ │ │ ├── glyphicons-halflings-regular.ttf │ │ │ ├── glyphicons-halflings-regular.woff │ │ │ └── glyphicons-halflings-regular.woff2 │ │ ├── img │ │ │ └── qiime2-rect-200.png │ │ └── js │ │ │ ├── bootstrap.min.js │ │ │ ├── child.js │ │ │ ├── jquery-3.2.0.min.js │ │ │ └── parent.js │ ├── qiime_16s_pipeline_Qiime1.8.pl │ ├── qiime_pipeline.pl │ ├── qiime_pipeline.py │ └── scripts │ │ ├── UPARSE_pick_otu.pl │ │ ├── drive5_py │ │ ├── die.py │ │ ├── die.pyc │ │ ├── faqual2fastq.py │ │ ├── faqual2fastq2.py │ │ ├── fasta.py │ │ ├── fasta.pyc │ │ ├── fasta_number.py │ │ ├── fastq.py │ │ ├── fastq_strip_barcode_relabel.py │ │ ├── fastq_strip_barcode_relabel2.py │ │ ├── primer.py │ │ ├── progress.py │ │ ├── progress.pyc │ │ ├── revcomp_lib.py │ │ ├── uc.py │ │ ├── uc.pyc │ │ ├── uc2otutab.py │ │ └── uc2otutab_mod.py │ │ ├── substract_no_template_control.pl │ │ └── test.pl ├── runReadsToContig.pl ├── runReadsToGenome.pl ├── samclip ├── send_notifications.py ├── specialty_genes │ ├── ProcessARRGIJson.py │ ├── ProcessARRGIResults.py │ ├── ProcessVFSBResults.py │ ├── ShortBred_convert_to_gff.pl │ ├── ShortBred_report.pl │ └── gff_to_faa.py ├── sra2fastq.pl ├── svg2pdf ├── svg2png ├── tab2Json_for_dataTable.pl ├── tbl2asn ├── upstream-coords.awk ├── usage_env.yml ├── variant_diff.pl ├── vcfutils.pl └── watch_bokeh_log.py ├── start_edge_ui.sh ├── testData ├── Ecoli_10x.1.fastq ├── Ecoli_10x.2.fastq ├── Reference │ ├── NC_000913.fna │ └── NC_000913.gbk ├── adapters.fasta ├── config.txt ├── contigs.fa ├── primers.fa ├── runAllTest.sh ├── runAssemblyTest │ ├── config.txt │ └── runTest.sh ├── runContigs2ReferenceTest │ ├── TestOutput2 │ │ └── ReadsBasedAnalysis │ │ │ └── readsMappingToRef │ │ │ ├── readsToRef.alnstats.txt │ │ │ ├── readsToRef.sort.bam │ │ │ ├── readsToRef.stats.pdf │ │ │ ├── readsToRef_plots.pdf │ │ │ └── runReadsToGenome.finished │ ├── config.txt │ ├── contigsToRef.log │ └── runTest.sh ├── runContigs2ReferneceTest │ ├── TestOutput2 │ │ └── ReadsBasedAnalysis │ │ │ └── readsMappingToRef │ │ │ ├── readsToRef.alnstats.txt │ │ │ ├── readsToRef.sort.bam │ │ │ ├── readsToRef.stats.pdf │ │ │ ├── readsToRef_plots.pdf │ │ │ └── runReadsToGenome.finished │ ├── config.txt │ ├── contigsToRef.log │ └── runTest.sh ├── runContigsAnnotationTest │ ├── config.txt │ ├── plot_gff3.log │ └── runTest.sh ├── runContigsTaxonomyTest │ ├── config.txt │ ├── runTest.sh │ ├── summary_by_topHitCount.txt │ └── summary_by_topHitCount2.txt ├── runDETEQtTest │ ├── IPC100fg_S56_L001_R1_001.fastq.gz │ ├── IPC100fg_S56_L001_R2_001.fastq.gz │ ├── NTC_S62_L001_R1_001.fastq.gz │ ├── NTC_S62_L001_R2_001.fastq.gz │ ├── S1-10K_S13_L001_R1_001.fastq.gz │ ├── S1-10K_S13_L001_R2_001.fastq.gz │ ├── S2-10K_S27_L001_R1_001.fastq.gz │ ├── S2-10K_S27_L001_R2_001.fastq.gz │ ├── Serum_S49_L001_R1_001.fastq.gz │ ├── Serum_S49_L001_R2_001.fastq.gz │ ├── config.txt │ ├── report.txt │ ├── runTest.sh │ ├── sample_test.txt │ └── targeted_reference.fa ├── runHostRemovalTest │ ├── config.txt │ ├── hostclean.stats.txt │ └── runTest.sh ├── runJoinPETest │ ├── JoinPE.log │ ├── config.txt │ └── runTest.sh ├── runNanoEDGETest │ ├── NC_001416.1.fasta │ ├── NanoStats.txt │ ├── config.txt │ ├── lambda.fastq.gz │ ├── readsToContigs.alnstats.txt │ ├── readsToContigs.alnstats2.txt │ ├── readsToContigs.alnstats3.txt │ ├── readsToRef.alnstats.txt │ ├── readsToRef.alnstats2.txt │ └── runTest.sh ├── runPCRassayTest │ ├── config.txt │ ├── contigs.fa │ ├── pcrContigValidation.txt │ └── runTest.sh ├── runPhageFinderTest │ ├── config.txt │ ├── contigs.fa │ ├── phageFinder_summary.txt │ └── runTest.sh ├── runPhylogeneticAnalysisTest │ ├── basesUsed.txt │ ├── config.txt │ ├── ebola_R1.fastq │ ├── ebola_R2.fastq │ ├── ebola_contigs │ ├── runTest.sh │ ├── testPhylogeneticAnalysis_summaryStatistics.txt │ └── testPhylogeneticAnalysis_summaryStatistics2.txt ├── runQCTest │ ├── QC.stats.txt │ ├── config.txt │ └── runTest.sh ├── runQiimeTest │ ├── QiimeTestGUI.png │ ├── barcodes.fastq.gz │ ├── biom_table_summary.txt │ ├── config.txt │ ├── forward_reads.fastq.gz │ ├── map.txt │ └── runTest.sh ├── runReads2ContigsTest │ ├── config.txt │ ├── readsToContigs.alnstats.txt │ └── runTest.sh ├── runReads2ReferenceTest │ ├── config.txt │ ├── readsToRef.alnstats.txt │ ├── readsToRef.alnstats2.txt │ └── runTest.sh ├── runReadsTaxonomyTest │ ├── config.txt │ ├── runTest.sh │ ├── summary.txt │ ├── summary2.txt │ ├── summary3.txt │ ├── summary4.txt │ ├── summary5.txt │ ├── summary6.txt │ ├── summary7.txt │ └── summary8.txt ├── runReportTest │ ├── config.txt │ └── runTest.sh ├── runSRADownloadTest │ ├── config.txt │ ├── fastqCount.txt │ └── runTest.sh ├── runSpecialtyGenesProfilingTest │ ├── AR_genes_ShortBRED_table.txt │ ├── Profiling_AR_genes_rgi.txt │ ├── Profiling_AR_genes_rgi2.txt │ ├── Profiling_AR_genes_rgi3.txt │ ├── VF_genes_ShortBRED_table.txt │ ├── VF_genes_ShortBRED_table2.txt │ ├── config.txt │ └── runTest.sh ├── runTest.sh └── runVariantAnalysisTest │ ├── TestOutput2 │ └── ReadsBasedAnalysis │ │ └── readsMappingToRef │ │ ├── readsToRef.alnstats.txt │ │ ├── readsToRef.gaps │ │ ├── readsToRef.sort.bam │ │ ├── readsToRef.stats.pdf │ │ ├── readsToRef.vcf │ │ ├── readsToRef_plots.pdf │ │ └── runReadsToGenome.finished │ ├── config.txt │ ├── readsToRef.SNPs_report.txt │ └── runTest.sh └── userManagement ├── client ├── edgeWSClientAdminGetProjects.pl ├── edgeWSClientAdminGetUsers.pl ├── edgeWSClientAdminProjectUpdate.pl ├── edgeWSClientGetProjectInfo.pl ├── edgeWSClientGetProjects.pl ├── edgeWSClientGetUserInfo.pl ├── edgeWSClientGuestGetProjectInfo.pl ├── edgeWSClientHello.pl ├── edgeWSClientLogin.pl ├── edgeWSClientProjectAdd.pl ├── edgeWSClientProjectGetGuests.pl ├── edgeWSClientProjectPublish.pl ├── edgeWSClientProjectShare.pl ├── edgeWSClientProjectUnpublish.pl ├── edgeWSClientProjectUnshare.pl └── edgeWSClientProjectUpdate.pl ├── createAdminAccount.pl ├── install_um_centOS.txt ├── install_um_ubuntu.txt ├── mariadb-java-client-1.2.0.jar ├── 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