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/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/merging/x
examples/merging/merged/miseq_partial_overlap_pair-QUALITY_PASSED_R1.fastq
examples/merging/merged/miseq_partial_overlap_pair-QUALITY_PASSED_R2.fastq
examples/merging/merged/miseq_partial_overlap_pair-STATS.txt
examples/v6-complete-overlap/ecoli-V6-R1.fastq
examples/v6-complete-overlap/ecoli-V6-R2.fastq
examples/v6-complete-overlap/sample-description.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_STATS
examples/v6-complete-overlap/output/E.coli_MERGED_V6_PRIMERS_REMOVED
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-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-gen-matching-fastq-files
scripts/iu-interleave-fastq
scripts/iu-merge-pairs
scripts/iu-remove-ids-from-fastq
scripts/iu-subsample-fastq
scripts/iu-trim-V6-primers
scripts/iu-trim-fastq
scripts/iu-visualize-mismatch-distribution
scripts/iu-visualize-plot-dicts
scripts/iu-visualize-qual-dicts