├── .gitignore ├── COPYING ├── IlluminaUtils ├── VERSION ├── __init__.py ├── _version.py ├── lib │ ├── __init__.py │ ├── fastalib.py │ └── fastqlib.py ├── rapidmerge.py └── utils │ ├── __init__.py │ ├── helperfunctions.py │ ├── runconfiguration.py │ └── terminal.py ├── MANIFEST.in ├── README.md ├── examples ├── demultiplexing.sh ├── demultiplexing │ ├── barcode_to_sample.txt │ ├── index.fastq │ ├── r1.fastq │ └── r2.fastq ├── info.sh ├── interleave_deinterleave.sh ├── merging │ ├── general-config-SAMPLE.ini │ ├── hiseq_complete_overlap_config-SAMPLE.ini │ ├── hiseq_complete_overlap_pair_1.fa │ ├── hiseq_complete_overlap_pair_2.fa │ ├── hiseq_partial_overlap_config-SAMPLE.ini │ ├── hiseq_partial_overlap_pair_1.fa │ ├── hiseq_partial_overlap_pair_2.fa │ ├── miseq_partial_overlap_config-SAMPLE.ini │ ├── miseq_partial_overlap_pair_1.fa │ └── miseq_partial_overlap_pair_2.fa ├── v6-complete-overlap.sh └── v6-complete-overlap │ ├── ecoli-V6-R1.fastq │ ├── ecoli-V6-R2.fastq │ └── sample-description.txt ├── pyproject.toml ├── requirements.txt ├── scripts ├── iu-compute-qual-dicts-from-fastq ├── iu-deinterleave-fastq ├── iu-demultiplex ├── iu-fasta-to-fastq ├── iu-fastq-to-fasta ├── iu-filter-merged-reads ├── iu-filter-quality-bokulich ├── iu-filter-quality-minoche ├── iu-gen-configs ├── iu-gen-matching-fastq-files ├── iu-interleave-fastq ├── iu-merge-pairs ├── iu-remove-ids-from-fastq ├── iu-subsample-fastq ├── iu-trim-V6-primers ├── iu-trim-fastq ├── iu-visualize-mismatch-distribution ├── iu-visualize-plot-dicts └── iu-visualize-qual-dicts ├── setup.cfg └── setup.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/merenlab/illumina-utils/HEAD/.gitignore -------------------------------------------------------------------------------- /COPYING: -------------------------------------------------------------------------------- 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