Code for analysis of minor allele distributions in Chlamydia trachomatis pull-down genome sequencing project
The original input files were created from mpileup output of Ct genomes mapped against the serovar D genome
MAP_file_pipeline script was used to create plots
Inputs - mpileup files
Outputs MAP_files.
One of the columns in the MAP_file report is called "regular", which reports the discrepancy between the total coverage and the sum of the reads mapped to the referecne+ other allels. This is essentially a report of possibly mismatched bases.
analyzing_MAP_pipeline_results.Rmd
Inputs MAP_files and reports stats about iSNPs(SNVs).
Outputs the Pos_count.tsv file for the numbers of times each iSNP occurs in the 87 original high_quality samples.
snippy_analysis.Rmd identifies the canonical (cSNPs) and
outputs lists of positions that discriminate T1 and T2 clades including T1T2_denovo_snps
fastGEAR_ancrestral_recombination and fastgear_recent_recombination pipelines analyse the output of fastGEAR analysis and make plots and gather stats. Als produce the fastgear_fiji_recombs file of recombinant positions.
SNP_pipelines analyzes SNPs for each strain
INputs are ``Pos_count.tsv, fastgear_fiji_recombs```,```MAP_files```, and ```T1T2_denovo_snps```, and ```2021_08_24-Grand_Summary - MAP_analysis_summary.tsv```.
Outputs are ```iSNPs_by_subject``` and ```iSNP_analysis_table```., and various plots
SNP_analysis_figures is similar to SNP_pipelines but updated figures for publications.
common_iSNPs.Rmd: Makes some plots.
inputs are /iSNPs_by_subject/.
counting_suppl_table1 scripts to analyze plasmids and ompA types in Supplementary Table 1.