.gitignore
CHANGELOG.md
COPYING
MANIFEST.in
README.md
VERSION
requirements.txt
setup.py
IlluminaUtils/__init__.py
IlluminaUtils/lib/__init__.py
IlluminaUtils/lib/fastalib.py
IlluminaUtils/lib/fastqlib.py
IlluminaUtils/utils/__init__.py
IlluminaUtils/utils/helperfunctions.py
IlluminaUtils/utils/runconfiguration.py
IlluminaUtils/utils/terminal.py
examples/demultiplexing.sh
examples/info.sh
examples/v6-complete-overlap.sh
examples/demultiplexing/barcode_to_sample.txt
examples/demultiplexing/index.fastq
examples/demultiplexing/r1.fastq
examples/demultiplexing/r2.fastq
examples/demultiplexing/output/00_DEMULTIPLEXING_REPORT
examples/demultiplexing/output/Sample_01-R1.fastq
examples/demultiplexing/output/Sample_01-R2.fastq
examples/demultiplexing/output/Sample_01.ini
examples/demultiplexing/output/Sample_02-R1.fastq
examples/demultiplexing/output/Sample_02-R2.fastq
examples/demultiplexing/output/Sample_02.ini
examples/demultiplexing/output/Sample_03-R1.fastq
examples/demultiplexing/output/Sample_03-R2.fastq
examples/demultiplexing/output/Sample_03.ini
examples/demultiplexing/output/Sample_04-R1.fastq
examples/demultiplexing/output/Sample_04-R2.fastq
examples/demultiplexing/output/Sample_04.ini
examples/demultiplexing/output/Sample_05-R1.fastq
examples/demultiplexing/output/Sample_05-R2.fastq
examples/demultiplexing/output/Sample_05.ini
examples/merging/.DS_Store
examples/merging/general-config-SAMPLE.ini
examples/merging/hiseq_complete_overlap_config-SAMPLE.ini
examples/merging/hiseq_complete_overlap_pair_1.fa
examples/merging/hiseq_complete_overlap_pair_2.fa
examples/merging/hiseq_partial_overlap_config-SAMPLE.ini
examples/merging/hiseq_partial_overlap_config.ini
examples/merging/hiseq_partial_overlap_pair_1.fa
examples/merging/hiseq_partial_overlap_pair_2.fa
examples/merging/miseq_partial_overlap_config-SAMPLE.ini
examples/merging/miseq_partial_overlap_config.ini
examples/merging/miseq_partial_overlap_pair_1.fa
examples/merging/miseq_partial_overlap_pair_2.fa
examples/v6-complete-overlap/ABN.11.AS.ini
examples/v6-complete-overlap/ABN.12.JL.ini
examples/v6-complete-overlap/ABN.12.LW.ini
examples/v6-complete-overlap/ABN.13.LW.ini
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examples/v6-complete-overlap/AS.14.CR8.1.2.2.ini
examples/v6-complete-overlap/AS.14.CR8.1.4.3.ini
examples/v6-complete-overlap/AS.14.CR8.1.4.4.ini
examples/v6-complete-overlap/AS.14.CR8.1.5.2.ini
examples/v6-complete-overlap/AS.14.CR8.1.5.4.ini
examples/v6-complete-overlap/AS.14.CR8.2.1.1.ini
examples/v6-complete-overlap/AS.14.CR8.2.1.4.ini
examples/v6-complete-overlap/AS.14.CR8.2.2.4.ini
examples/v6-complete-overlap/AS.14.CR8.2.3.3.ini
examples/v6-complete-overlap/AS.14.CR8.2.3.4.ini
examples/v6-complete-overlap/AS.14.CR8.2.4.1.ini
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examples/v6-complete-overlap/CRG.12.ASss.ini
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examples/v6-complete-overlap/CRGxPM.13.SW.ini
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examples/v6-complete-overlap/CWC.14.LS.ini
examples/v6-complete-overlap/DBP.13.KR.ini
examples/v6-complete-overlap/DBP.14.KR.ini
examples/v6-complete-overlap/E.coli.ini
examples/v6-complete-overlap/HBL.14.AH.SSE.ini
examples/v6-complete-overlap/HPI.09.LS.0.ini
examples/v6-complete-overlap/HPI.14.LS.0.ini
examples/v6-complete-overlap/LGS.14.TG.0.ini
examples/v6-complete-overlap/MAM.14.LF.CD.ini
examples/v6-complete-overlap/MBD.13.KR.ini
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examples/v6-complete-overlap/PC.14.CR8.1.1.2.ini
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examples/v6-complete-overlap/PMT.14.BG.0.ini
examples/v6-complete-overlap/RFF.12.RR.ini
examples/v6-complete-overlap/RFF.13.RR.ini
examples/v6-complete-overlap/SBB.02.TG.0.ini
examples/v6-complete-overlap/SFB.10.LS.ini
examples/v6-complete-overlap/Silk.13.OSU.1.ini
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examples/v6-complete-overlap/Soil.13.OSU.2.ini
examples/v6-complete-overlap/Soil.14.AS.1.ini
examples/v6-complete-overlap/Soil.14.AS.2.ini
examples/v6-complete-overlap/Soil.14.OSU.1.ini
examples/v6-complete-overlap/Soil.14.OSU.2.ini
examples/v6-complete-overlap/Soil.14.PC.1.ini
examples/v6-complete-overlap/TGS.13.TH.ini
examples/v6-complete-overlap/TGS.14.TH.0.ini
examples/v6-complete-overlap/WG1.ini
examples/v6-complete-overlap/WG10.ini
examples/v6-complete-overlap/WG2.ini
examples/v6-complete-overlap/WG3.ini
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examples/v6-complete-overlap/WG7.ini
examples/v6-complete-overlap/WG8.ini
examples/v6-complete-overlap/WG9.ini
examples/v6-complete-overlap/ctl.3ext.ini
examples/v6-complete-overlap/ctl.pooledCRN1.ini
examples/v6-complete-overlap/ecoli-V6-R1.fastq
examples/v6-complete-overlap/ecoli-V6-R2.fastq
examples/v6-complete-overlap/plate2ctl1.ini
examples/v6-complete-overlap/plate2ctl2.ini
examples/v6-complete-overlap/plate2ctl3.ini
examples/v6-complete-overlap/plate2ctl4.ini
examples/v6-complete-overlap/plate3ctl1.ini
examples/v6-complete-overlap/plate3ctl2.ini
examples/v6-complete-overlap/plate3ctl3.ini
examples/v6-complete-overlap/plate3ctl4.ini
examples/v6-complete-overlap/sample-description.txt
examples/v6-complete-overlap/sample_r1_r2_revised.txt
examples/v6-complete-overlap/seed.AS.CTL.ini
examples/v6-complete-overlap/seed.OSU.Ctrl 2of4.ini
examples/v6-complete-overlap/seed.OSU.Ctrl 2of5.ini
examples/v6-complete-overlap/seed.OSU.ctrl.ini
examples/v6-complete-overlap/seed.PC.CTL.ini
examples/v6-complete-overlap/xx.txt
examples/v6-complete-overlap/output/E.coli-QUALITY_PASSED_R1.fastq
examples/v6-complete-overlap/output/E.coli-QUALITY_PASSED_R2.fastq
examples/v6-complete-overlap/output/E.coli-READ_IDs.cPickle.z
examples/v6-complete-overlap/output/E.coli-STATS.txt
examples/v6-complete-overlap/output/E.coli.ini
examples/v6-complete-overlap/output/E.coli_FAILED
examples/v6-complete-overlap/output/E.coli_FAILED_WITH_Ns
examples/v6-complete-overlap/output/E.coli_MERGED
examples/v6-complete-overlap/output/E.coli_MERGED-MAX-MISMATCH-0
examples/v6-complete-overlap/output/E.coli_MISMATCHES_BREAKDOWN
examples/v6-complete-overlap/output/E.coli_STATS
illumina_utils.egg-info/PKG-INFO
illumina_utils.egg-info/SOURCES.txt
illumina_utils.egg-info/dependency_links.txt
illumina_utils.egg-info/requires.txt
illumina_utils.egg-info/top_level.txt
scripts/iu-analyze-v6-complete-overlaps
scripts/iu-compute-qual-dicts-from-fastq
scripts/iu-demultiplex
scripts/iu-fastq-to-fasta
scripts/iu-filter-merged-reads
scripts/iu-filter-quality-bokulich
scripts/iu-filter-quality-minoche
scripts/iu-gen-configs
scripts/iu-merge-pairs
scripts/iu-remove-ids-from-fastq
scripts/iu-trim-fastq
scripts/iu-visualize-mismatch-distribution
scripts/iu-visualize-plot-dicts
scripts/iu-visualize-qual-dicts