├── .gitignore ├── 2017_project_6.Rproj ├── Brewfile ├── LICENSE ├── Makefile ├── MolecEst └── MolecLenEst.py ├── README.md ├── SHA256 ├── _config.yml ├── aligner_benchmarks ├── README.md └── timing.txt ├── chromeqc-logo.png ├── chrometools ├── data └── README.md ├── extract_barcodes ├── README.md └── extract_barcodes.awk ├── hg002g1_lrwgsvc └── outs │ ├── summary.csv │ └── summary.png ├── hg003g1_lrwgsvc └── outs │ └── summary.csv ├── hg004g1_lrwgsvc └── outs │ └── summary.csv ├── minimap2_format.py ├── multiqc ├── README.md ├── hg002_chromqc_molecule_size.csv ├── hg002g1_basic_summary.csv ├── hg003_chromqc_molecule_size.csv ├── hg003g1_basic_summary.csv ├── hg004g1.lrbasic.bwa.sortbx.molecule.100.tsv ├── multiqc_config_chromeqc.yaml ├── multiqc_config_longranger.yaml ├── multiqc_data_chromeqc │ └── multiqc_sources.txt ├── multiqc_data_longranger │ └── multiqc_sources.txt ├── multiqc_report_chromeqc.html ├── multiqc_report_longranger.html ├── preprocess.py ├── preprocess.sh ├── preprocess_chromeqc.sh ├── subset1_unmatched_barcodes_population_counts.tsv └── subset1_whitelist_barcodes_population_counts.tsv ├── off_by_one └── cross_ref_whitelist_stats.py ├── paper.bib ├── paper.csl ├── paper.doi ├── paper.md ├── report ├── SummaryReport.rmd ├── SummaryReport_GettingStarted.rmd ├── SummaryReportv2 ├── report.rmd └── summary.rmd ├── requirements.txt ├── select_random_subset ├── README.md ├── adapter_16mers.py ├── adapters.fa ├── process_fastq.py ├── random_sampling_from_whitelist.py ├── subset_barcodes.pdf ├── subset_barcodes_population_counts.tsv ├── subset_barcodes_top_barcodes.tsv ├── unmatched_barcodes.pdf ├── unmatched_barcodes_population_counts.tsv ├── unmatched_barcodes_top_barcodes.tsv ├── whitelist_barcodes_population_counts.tsv └── whitelist_barcodes_top_barcodes.tsv ├── slides-figure ├── chromeQC.png ├── loupe_summary_page_GEM.png ├── loupe_summary_page_input_DNA.png ├── mutltiQC.png └── unnamed-chunk-2-1.png ├── slides.Rpres ├── slides.css └── 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