vikash84's Projects
Materials for Analyzing Next-Generation Sequencing (ANGUS) course.
A tool for drawing ANI clustermap between all-vs-all microbial genomes using fastANI & seaborn
APP serotyping pipeline based on the modification of the SsuisSerotyping pipeline by Taryn B. T. Athey
Applied Computational Genomics Course at UU: Spring 2018
Comprehensive resistance detection from WGS data
Use python's argparse module in shell scripts
A scalable bacterial genome assembly, annotation and analysis pipeline
Automated Sanger Analysis Pipeline (ASAP): a tool for rapidly analyzing Sanger sequencing data with minimum user interference.
A tool for removing redundant genomes from a set of assemblies
ATLAS - Three commands to start analysing your metagenome data
A wrapper to run ATLAS within a Docker container
Materials for ATS 2021 PG11: A HANDS-ON INTRODUCTION TO STUDYING THE LUNG MICROBIOME
Pipeline components for real-time phylodynamic analysis
Nextflow implementation of Nextstrain's Augur pipeline
A short analysis of Oxford Nanopore consensus accuracy for bacterial genome assemblies
An automated pipeline working on metagenomics analyses of mosquito virome
Example Python scripts for automating workflows (primarily with MS Office products on Windows)
Autometa: Automated Extraction of Genomes from Shotgun Metagenomes
Awesome resources on Bioinformatics, data science, machine learning, programming language (Python, Golang, R, Perl) and miscellaneous stuff.
A curated list of awesome READMEs
A curated list of reproducible research case studies, projects, tutorials, and media
Generic pipeline for prokaryotic genome annotation
a collection of scripts for organising bacterial genomes by species
In this training course you will find theory and practice material for introducing yourself to wgs analysis for bacterial, including outbreak investigation.
A flexible pipeline for complete analysis of bacterial genomes
BACTpipe: An assembly and annotation pipeline for bacterial genomics