vikash84's Projects
Determine which reference sequence is more likely to be present in a given sample
script for identification of S. suis serotype from draft genome
SHAMAN is a SHiny application for Metagenomic ANalysis including a bioinformatic workflow, the statistical analysis and multiple visualization.
A Shotgun Metagenome Annotation Pipeline
Scripts and notes for singularity containers used for bioinformatics analyses
Webinars&Tutorial on Containers on HPC and Cloud with Singularity
Materials for 3 hour hands-on workshop entitled "Creating and running software containers with Singularity"
Fast, robust ANI and aligned fraction for metagenomic genomes and contigs
smallgenomeutilities is a collection of Python scripts to convert alignments between different reference genomes.
R notebooks containing the code used to analyze Smart-seq-total data
Simple Manipulation Of Trees
Produce the nullarbor report for clinical microbiologists using snakemake
A toolkit based on snakemake and python for analysis of NGS data
Identify and remove adapter/systemic contamination in WGS and metagenomic sequencing DNA/RNA data.
Finds SNP sites from a multi-FASTA alignment file
Takes a VCF and applies annotations from a GFF using SnpEff
sequencing data analysis pipelines
Perform spa typing on Staphylococcus aureus assemblies or reads.
SPANDx - Comparative genomics for next-generation haploid sequence data
SPAR is a collection of python scripts useful for the analysis of swine pathogen genomes.
A complete pipeline for metagenomic analysis
An integrated analysis pipeline for Streptococcus suis
Rapid Streptococcus suis Serotyping on Nanopore Sequencing Data