├── .gitignore ├── README.md ├── data-processing.Rproj ├── lcwgs_data_processing.md ├── markdowns ├── adapter_clipping.Rmd ├── adapter_clipping.md ├── deduplicate_clipoverlap.Rmd ├── deduplicate_clipoverlap.md ├── low_coverage_mapping.Rmd ├── low_coverage_mapping.md ├── quality_filtering.Rmd └── quality_filtering.md └── scripts ├── .Rhistory ├── adapter_clipping.sh ├── adapter_clipping.slurm ├── build_bowtie_ref_index.sh ├── convert_count_to_presence.awk ├── count_bam_merged.sh ├── count_bam_unmerged.sh ├── count_depth_per_position_all_samples.sh ├── count_depth_per_position_per_sample.sh ├── count_fastq.sh ├── count_species.pl ├── deduplicate_clipoverlap.sh ├── deduplicate_clipoverlap.slurm ├── fastq_species_detector.sh ├── low_coverage_mapping.sh ├── low_coverage_mapping.slurm ├── quality_filtering.sh ├── quality_filtering.slurm ├── realign_indels.sh ├── rename_fastq.sh ├── rename_fastq_lower_case.sh ├── run_species_detector.sh ├── subsample_fastq.pl ├── sum_by_row.awk └── 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