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angus

Materials for Analyzing Next-Generation Sequencing (ANGUS) course.

aniclustermap

A tool for drawing ANI clustermap between all-vs-all microbial genomes using fastANI & seaborn

app_serotyping_pipeline

APP serotyping pipeline based on the modification of the SsuisSerotyping pipeline by Taryn B. T. Athey

applied-computational-genomics

Applied Computational Genomics Course at UU: Spring 2018

arbetsprov

ardap

Comprehensive resistance detection from WGS data

argparse-bash

Use python's argparse module in shell scripts

asap

A scalable bacterial genome assembly, annotation and analysis pipeline

asap-1

Automated Sanger Analysis Pipeline (ASAP): a tool for rapidly analyzing Sanger sequencing data with minimum user interference.

assembly-dereplicator

A tool for removing redundant genomes from a set of assemblies

atlas

ATLAS - Three commands to start analysing your metagenome data

atlas-wrapper

A wrapper to run ATLAS within a Docker container

atram

ats2021_pg11

Materials for ATS 2021 PG11: A HANDS-ON INTRODUCTION TO STUDYING THE LUNG MICROBIOME

augur

Pipeline components for real-time phylodynamic analysis

augur-nf

Nextflow implementation of Nextstrain's Augur pipeline

august-2019-consensus-accuracy-update

A short analysis of Oxford Nanopore consensus accuracy for bacterial genome assemblies

auto_metaviromics

An automated pipeline working on metagenomics analyses of mosquito virome

automation-examples

Example Python scripts for automating workflows (primarily with MS Office products on Windows)

autometa

Autometa: Automated Extraction of Genomes from Shotgun Metagenomes

awesome

Awesome resources on Bioinformatics, data science, machine learning, programming language (Python, Golang, R, Perl) and miscellaneous stuff.

awesome-readme

A curated list of awesome READMEs

awesome-reproducible-research

A curated list of reproducible research case studies, projects, tutorials, and media

bacannot

Generic pipeline for prokaryotic genome annotation

bacsort

a collection of scripts for organising bacterial genomes by species

bacterial_wgs_training

In this training course you will find theory and practice material for introducing yourself to wgs analysis for bacterial, including outbreak investigation.

bactopia

A flexible pipeline for complete analysis of bacterial genomes

bactpipe

BACTpipe: An assembly and annotation pipeline for bacterial genomics

bactprep

bactsnp