From 4bdfcfff6300d95c8963de8da0238cb75b1a4157 Mon Sep 17 00:00:00 2001 From: Zoe Anne Dyson Date: Sat, 13 Nov 2021 12:45:27 +0000 Subject: [PATCH] Update README.md --- README.md | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 02fae42..0beace2 100644 --- a/README.md +++ b/README.md @@ -23,10 +23,14 @@ bash run_bcf_batches.sh Wong2015_Tanzania ``` ## What is in this repo? -**GHRU_SNV_Stats_Generator.py** - python script for extracting high (PASS) and low (LowQual) SNV calls from bcf files produced by the GHRU mapping pipeline. -**CT18_repeats_phages_excluded_regions.tsv** - Phage and repeat regions normally excluded from phylogenetic analysis of S. Typhi (CT18: accession no. AL513382). -**run_ghru_snv_stats_in_batches.sh** - wrapper script for batch submission of jobs via lsf cluster system. -**Plot_Low_Qual_SNV_Distribution.R** - example R plotting script - visualises the distribution of low qual SNV calls throughout the reference sequence both before an after the removal of those falling within repetitive and phage regions (normally excluded for phylogenetic analysis). +**GHRU_SNV_Stats_Generator.py** - python script for extracting high (PASS) and low (LowQual) SNV calls from bcf files produced by the GHRU mapping pipeline.\ + +**CT18_repeats_phages_excluded_regions.tsv** - Phage and repeat regions normally excluded from phylogenetic analysis of S. Typhi (CT18: accession no. AL513382).\ + +**run_ghru_snv_stats_in_batches.sh** - wrapper script for batch submission of jobs via lsf cluster system.\ + +**Plot_Low_Qual_SNV_Distribution.R** - example R plotting script - visualises the distribution of low qual SNV calls throughout the reference sequence both before an after the removal of those falling within repetitive and phage regions (normally excluded for phylogenetic analysis).\ +