Scripts for PHL pathogen genomic data
May 17th 2018 - June 28th 2018 (Vincent Caruso -- carusov)
August 17th 2018 - December 14th 2018 (Mark Klick -- markklick206)
This bioinformatic pipeline consists of several computational modules: Quality Control Pipeline, Computational Species Typing, Virulence/Antimicrobial Resistance Pipeline, and Isolate Relatedness Analysis Pipeline. Each module consists of multiple steps which utilize an array of state-of-the-art open source software tools. These open-source software tools are recommended, used, and considered the best-practices by a consensus of bioinformaticians within and outside of the public health domain
QC PIPELINE
CG-Pipeline https://github.com/lskatz/CG-Pipeline
Software tools
run_assembly_shuffleReads.pl
run_assembly_trimClean.pl
Contamination Check
Software tools
Kraken https://ccb.jhu.edu/software/kraken/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053813/
Read Metrics
Software tools
run_assembly_readMetrics.pl
Cluster density
Q30
Average read length
Depth of sequencing coverage
Computational Species Typing Pipeline
Salmonella
Software tools
MASH https://github.com/marbl/Mash/releases
SeqSero https://github.com/denglab/SeqSero
Isolate Relatedness Analysis Pipeline
Determine Reference Assembly
Software tools
CLC BIO
Find Best Match reference sequence based on kmer spectra
pulseNETplus reference sequence/assembly database
MASH https://github.com/marbl/Mash/releases
hqSNP Analysis
Software tools
LyveSet 1.1.4f https://github.com/lskatz/lyve-SET
Phylogeny/dendrogram of how isolates cluster Pairwise SNP Matrix FigTree
LYVE-SET Overview:
0: Read Cleaning
https://github.com/lskatz/CG-Pipeline/blob/master/scripts/run_assembly_trimClean.pl
1: Mapping Sequencing Reads to a Reference Genome
https://www.sanger.ac.uk/science/tools/smalt-0
2: Variant detection, i.e., detecting SNPs
http://varscan.sourceforge.net/
Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, & Ding L (2009). VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics (Oxford, England), 25 (17), 2283-5 PMID: 19542151
3: Creating the Phylogenetic tree/ dendogram
https://sco.h-its.org/exelixis/web/software/raxml/index.html
A. Stamatakis: "RAxML Version 8: A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies". In Bioinformatics, 2014, open access.
OSPHL LYVE-SET Overview:
Github https://github.com/carusov/nasty-bugs
-1: Download Sequencing files
https://github.com/carusov/nasty-bugs/tree/master/scripts/download%20scripts
0: Read Cleaning and trimming
https://github.com/carusov/nasty-bugs/blob/master/scripts/Filtering%20and%20decontamination/trim_and_clean.sh
1: Running Lyve-SET!
https://github.com/carusov/nasty-bugs/blob/master/scripts/SNP%20scripts/add_reads_lyveset.sh