Current collection include the following -

• 1000gpca.py (1000 Genomes Project)
• TSNE.py
• categorized_gramox.py
• combine_data.py
• common_seqs_count.py
• correlation.py
• count_ChrX_variants.py (1000 Genomes Project)
• count_singletons.py (1000 Genomes Project)
• count_variants.py (1000 Genomes Project)
• count_variant_sites.py   (1000 Genomes Project)
• craigslist_search.py
• dissimilarity_overlap_curve.py
• fill_empty_gramox_data.py
• get_core_ids.py
• get_fastq_quality_stats.py
• gramox_calc.py
• gramox_to_itol_color.py
• grep_count_seqs.py
• haploid_local_ancestry_inference.py (1000 Genomes Project)
• merge_hap_htz_counts.py (1000 Genomes Project)
• merge_with_pear.py
• otu_metadata_db.py
• overlap_comparisons.py
• pct_abd_gramox.py
  • In process of moving to PhyloToAST repo.
• plot_MA.py
• plot_ancestry.py
• plot_autosomal_heterozygosity.py (1000 Genomes Project)
• plot_heterozygosity.py (1000 Genomes Project)
• remove_duplicate_genes.py
• run_merge_cmd.py
• run_qual_filter_cmd.py
• trim_five_prime_end_adapters.py
• trim_three_prime_end_adapters.py

• LDA.R
• PCA.R

• concat_R1_R2_files.sh
• get_R1_R2_md5.sh
• runpy.sh