mcan_popgen

This repository includes scripts and data supporting a comparitive population genomics of Mycobacterium canettii and Mycobacterium tuberculosis (Jensen Lab, ASU).

Repository structure

• consensus_sequence_processing
  • trimmomatic.sh: Adapter and quality trimming used on raw MCAN sequencing data
  • bwa_snippymem.sh: Alignment script based on parameters set in the Snippy pipeline for optimal bacterial consensus calling
  • freebayes.sh: SNP calling and filtering script
  • bcftools_consensus.sh: Consensus calling script
  • full.multi.fasta.gz: Compressed multi-fasta file containing the consensus sequences for all MCAN samples in analysis
• ldhat_results
  • mcan
    • mcan_ldhat_convert.sh: Command line for LDhat-convert, which produced the "sites.txt" and "locs.txt" files used as input for LDhat-pairwise.
    • outfile.txt: Results of LDhat-pairwise run on the MCAN dataset
  • simulations
    • base
      • er_convert.sh
      • er_pw.sh
      • er.[0..99].pw.outfile.txt
      • pairwise_stats.txt
    • base_bn
      • er_bn_convert.sh
      • er_bn_pw.sh
      • er_bn.[0..99].pw.outfile.txt
      • pairwise_stats.txt
    • base_bn_dfe
      • er_bn_dfe_convert.sh
      • er_bn_dfe_pw.sh
      • er_bn_dfe.[0..99].pw.outfile.txt
      • pairwise_stats.txt
    • base_dfe
      • er_dfe_convert.sh
      • er_dfe_pw.sh
      • er_dfe.[0..99].pw.outfile.txt
      • pairwise_stats.txt
    • base_psi
      • er_psi_convert.sh
      • er_psi_pw.sh
      • er_psi.[0..99].pw.outfile.txt
      • pairwise_stats.txt
    • base_psi_bn
      • er_psi_bn_convert.sh
      • er_psi_bn_pw.sh
      • er_psi_bn.[0..99].pw.outfile.txt
      • pairwise_stats.txt
    • base_psi_bn_dfe
      • er_psi_bn_dfe_convert.sh
      • er_psi_bn_dfe_pw.sh
      • er_psi_bn_dfe.[0..99].pw.outfile.txt
      • pairwise_stats.txt
    • base_psi_dfe
      • er_psi_dfe_convert.sh
      • er_psi_dfe_pw.sh
      • er_psi_dfe.[0..99].pw.outfile.txt
      • pairwise_stats.txt
• simulations
  • fasta_to_consensus.py
  • base
    • base.slim
  • base_bn
    • base_bn.slim
  • base_bn_dfe
    • base_bn_dfe.slim
  • base_dfe
    • base_dfe.slim
  • base_psi
    • base_psi.slim
  • base_psi
    • base_psi.slim
  • base_psi_bn
    • base_psi_bn.slim
  • base_psi_bn_dfe
    • base_psi_bn_dfe.slim
  • base_psi_dfe
    • base_psi_dfe.slim
• within_host_diversity_processing
  • traunerPipe_scythe_sickle.sh
  • within_host_variation_alignment.sh
  • traunerPipe_ps_Serial_Deepseq_Variant_calling.sh
  • mcan
    • mcan_snp_counts.txt: Low frequency SNP counts per sample.
    • mcan_filter_snp_files
      • [sample_name].filter.snp: Each file contains the filtered low frequency SNP positions and nucleotides for a given sample.
  • mtbc
    • mtbc_snp_counts.txt: Low frequency SNP counts per sample.
    • mtbc_filter_snp_files
      • [sample_name].filter.snp: Each file contains the filtered low frequency SNP positions and nucleotides for a given sample.