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2023-june-introduction-to-r-for-bioinformatics

An introduction to the basic R programming for biologists. No data analysis experience necessary! Participants will gain skills necessary to run basic statistical analyses and generate figures in R.

abritamr

A pipeline for running AMRfinderPlus and collating results into functional classes

api_hackathon

apibuilding

apirandom

argprofiler

A pipeline for for large-scale analysis of antimicrobial resistance genes and their flanking regions in metagenomic datasets

atlas

ATLAS - Three commands to start analyzing your metagenome data

carbon

:black_heart: Create and share beautiful images of your source code

cgeisolate

CGE isolate pipeline

chemicalassettracker

The Chemical Asset Tracker is a web application that facilitates tracking and reporting on chemical inventories.

conda

OS-agnostic, system-level binary package manager and ecosystem

dart

dart-hackathon-repository

dorado

A LibTorch Basecaller for Oxford Nanopore Reads

fastmlst

⚡️🧬 FastMLST: A multi-core tool for multilocus sequence typing of draft genome assemblies

fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

feb-2024-pythonhack2

feb_2024-python-hackathon1

fieldbioinformatics

The ARTIC field bioinformatics pipeline

filtlong

quality filtering tool for long reads

flye

De novo assembler for single molecule sequencing reads using repeat graphs

git-and-github-masterclass---the-practical-bootcamp

Git an GitHub Masterclass - The Practical Bootcamp, by Packt Publishing

git-tutorial

A tutorial (slides, code) for Git and Github for Scientists

gottcha

Accurate read-based metagenome characterization using a hierarchical suite of unique signatures. Please visit our homepage:

ilri-africa-cdc-training

A suite of pathogen genomics tutorials for the ILRI Genomics platform training programs

kcri-cge-bap

KCRI CGE Bacterial Analysis Pipeline

kleborate

kraken-protocol

Metagenome analysis using the Kraken software suite

kraken2

The second version of the Kraken taxonomic sequence classification system

lathe

A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing