├── .gitignore ├── LICENSE ├── README.md ├── config.sh ├── data ├── 50.00p-HG002.maternal_50.00p-FDA-ARGO-41_sim_SUB-h100000-m100000_R1.fastq.gz └── 50.00p-HG002.maternal_50.00p-FDA-ARGO-41_sim_SUB-h100000-m100000_R2.fastq.gz ├── filter.array.sbatch ├── filter.sh ├── filter_align_hg38.sh ├── filter_align_hprc.sh ├── filter_align_t2t.sh ├── filter_fastp.sh ├── filter_index_hprc.sh ├── generate_stats.sh ├── human-filtration.yml ├── ref ├── NC_001422.fna └── known_adapters.fna ├── scripts ├── create_minimap2_indexes.sh ├── create_movi_index.sh ├── download_references.sh ├── filter_pmls.py ├── hf_filter_pmls.py ├── pair.py └── qiita_filter_pmls.py ├── split_fastq.sh ├── submit_filter.array.sh └── tests ├── __init__.py ├── test_filter_pmls.py ├── test_pipeline.py └── test_qiita_filter_pmls.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cguccione/human_host_filtration/HEAD/.gitignore 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