├── .clang-format ├── .gitattributes ├── .github ├── PULL_REQUEST_TEMPLATE.md ├── release_checklist.md └── workflows │ └── ci.yml ├── .gitignore ├── .gitmodules ├── .pre-commit-config.yaml ├── .readthedocs.yml ├── CHANGELOG.rst ├── CITATION.cff ├── LICENSE ├── MANIFEST.in ├── README.rst ├── codecov.yml ├── docs ├── _static │ └── images │ │ ├── doi_image.svg │ │ ├── fingerprint.fodg │ │ ├── fingerprint.svg │ │ ├── overrepresented_sampling.fodg │ │ └── overrepresented_sampling.svg ├── conf.py ├── includes │ ├── CHANGELOG.rst │ ├── README.rst │ └── docs │ │ └── _static │ │ └── images │ │ └── doi_image.svg ├── index.rst ├── module_options.rst ├── reports │ ├── 21C125_R1.fastq.gz.html │ ├── GM24385_1.fastq.gz.html │ └── GM24385_1_cut.fastq.gz.html └── requirements-docs.txt ├── pyproject.toml ├── scripts ├── adapter_match_rates.py ├── benchmark_create_sequence_index.py ├── benchmark_sequence_identity.py ├── check_presence_in_fasta.py ├── fastq_create.py ├── finger_print_quality.py ├── fingerprinter.py ├── generate_colors.py ├── generate_nanopore_barcodes.py ├── oxford_nanopore_barcodes.tsv ├── oxford_nanopore_native_barcodes.tsv ├── run_sequali_paired.py └── score_to_error_rate.py ├── setup.py ├── src └── sequali │ ├── __init__.py │ ├── __main__.py │ ├── _qc.pyi │ ├── _qcmodule.c │ ├── _seqident.pyi │ ├── _seqidentmodule.c │ ├── adapters.py │ ├── adapters │ └── adapter_list.tsv │ ├── compiler_defs.h │ ├── contaminants │ ├── Illumina.fasta │ ├── README │ ├── UniVec.fasta │ ├── common_human_repeats.fasta │ ├── oxford_nanopore.fasta │ └── oxford_nanopore_barcodes.fasta │ ├── debug_vectors.h │ ├── murmur3.h │ ├── py.typed │ ├── report_modules.py │ ├── score_to_error_rate.h │ ├── sequence_identification.py │ ├── static │ ├── sequali_report.css │ └── svg_to_download_link.js │ ├── util.py │ └── wanghash.h ├── tests ├── __init__.py ├── data │ ├── 100_illumina_adapters.fastq │ ├── 100_nanopore_reads.fastq.gz │ ├── LTB-A-BC001_S1_L003_R1_001.fastq.gz │ ├── LTB-A-BC001_S1_L003_R1_001_names_changed.fastq.gz │ ├── LTB-A-BC001_S1_L003_R1_001_shortened.fastq.gz │ ├── LTB-A-BC001_S1_L003_R2_001.fastq.gz │ ├── LTB-A-BC001_S1_L003_R2_001_shortened.fastq.gz │ ├── README.md │ ├── dorado_nanopore_100reads.bam │ ├── empty.fastq │ ├── empty_illumina_metadata.fastq │ ├── empty_nanopore_metadata.fastq │ ├── empty_read.fastq │ ├── missing_quals.bam │ ├── missing_quals.sam │ ├── nanopore_disparate_dates.fastq │ ├── project.NIST_NIST7035_H7AP8ADXX_TAAGGCGA_1_NA12878.bwa.markDuplicates.bam │ ├── project.NIST_NIST7035_H7AP8ADXX_TAAGGCGA_1_NA12878.bwa.markDuplicates.sam │ ├── secondary_alignment.bam │ ├── simple.fastq │ ├── simple.raw.bam │ ├── simple.unaligned.bam │ ├── single_illumina_metadata.fastq │ ├── single_nanopore_metadata.fastq │ ├── single_nuc.fastq │ ├── test.fasta │ ├── test_skip.bam │ └── test_skip.sam ├── test_adapter_counter.py ├── test_bam_parser.py ├── test_dedup_estimator.py ├── test_fastq_parser.py ├── test_fastq_record_array.py ├── 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