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abricate

:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes

adegenet

adegenet: a R package for the multivariate analysis of genetic markers

adjutant

Runs a pubmed query, returns results and allows user to explore high-level structure of returned documents

ads1-notebooks

Copies of notebooks used in the practical sessions for Algorithms for DNA Sequencing

ads1-slides

Slides for Algorithms for DNA Sequencing Coursera class

an-introduction-to-applied-bioinformatics

Interactive lessons in bioinformatics.

aneuploidy_detection

Script uses simply alignment and a hard threshold for deviation in order to detect changes in coverage

applied-computational-genomics

Applied Computational Genomics Course at UU: Spring 2017

asap

Amplicon Sequencing Analysis Pipeline

asap-1

A scalable bacterial genome assembly, annotation and analysis pipeline

awesome-nextflow

A curated list of nextflow based pipelines

bacterialgwas

A pipeline for performing genome-wide association tests for bacterial genomes.

bam_coverage

Calculates coverage stats for a .bam mapping file.

bamqc

Mapped QC analysis program

basecalling-comparison

A comparison of different Oxford Nanopore basecallers

bbmap

(Not Offical) BBMap short read aligner, and other bioinformatic tools.

benchmark_microbiome_transformations

Code to reproduce the analyses from the paper "Benchmarking microbiome transformations favors experimental quantitative approaches to address compositionality and sampling depth biases"

bioawk

BWK awk modified for biological data

bioinfo_notebook

bioinformatics-ca.github.io

repository for student workshop pages

bioinformatics-training

Bioinformatics training resources

biom-format

The Biological Observation Matrix (BIOM) Format Project

biopieces

Biopieces is a bioinformatic framework of tools easily used and easily created.

biotyper

an R package to biotype a community

blobology

Tools for making blobplots or Taxon-Annotated-GC-Coverage plots (TAGC plots) to visualise the contents of genome assembly data sets as a QC step

blobtools-light

Light version of the upcoming blobtools package

centrifuge

Classifier for metagenomic sequences

checkm

Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes

clinker

Gene cluster comparison figure generator

coinfinder

A tool for the identification of coincident (co-occurring and avoiding) genes in pangenomes.