UG sub_lineage mutations drug resistant mutations discovery FastQC MultiQC Snippy Rapid Bacterial SNP Genotype and Drug Resistance Calling Version 1.0.0
Author Gerald Mboowa
Synopsis Snippy finds SNPs between a haploid reference genome and your HTS dataset. It will find both substitutions (snps) and insertions/deletions (indels). It will use as many CPUs as you can give it on a single computer. It is designed with speed in mind, and produces a consistent set of output files in a single folder (this has been tested with Snippy 4.3.2 (https://github.com/tseemann/snippy - Torsten Seemann) .
i. FastQC Aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines.
I. MultiQC Searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous FastQC reports
ii. Running Snippy for the Samples
iii. Running MTB Genotypes and Drug Resistance Annotations for the Samples
iv. Deleting all Redundant files generated
Output Files
Text files for ¬ MTB genotypes ¬ Drug resistance mutations both MDR and XDR
Issues Please submit suggestions and bug reports to the Issue Tracker
Requirements FastQC MultiQC Perl >= 5.12 Perl Modules: Time::Piece (core with modern Perl), Bioperl >= 1.6 bwa mem >= 0.7.12 minimap2 >= 2.0 samtools >= 1.7 bedtools >= 2.0 bcftools >= 1.7 GNU parallel >= 2013xxxx freebayes >= 1.1 (freebayes, freebayes-parallel, fasta_generate_regions.py) vcflib >= 1.0 (vcfstreamsort, vcfuniq, vcffirstheader) vt >= 0.5 readseq >= 2.0 snpEff >= 4.3 samclip >= 0.2 seqtk >= 1.2 snp-sites >= 2.0 wgsim >= 1.8 (for testing only - wgsim command) Bundled binaries Tested on macOS (compiled on macOS Mojave)