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atlas

ATLAS - Three commands to start analyzing your metagenome data

awesome-go

A curated list of awesome Go frameworks, libraries and software

barrnap

:microscope: :leo: Bacterial ribosomal RNA predictor

bbmap

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

bioconda-recipes

Conda recipes for the bioconda channel.

bioinformatics

cat

CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)

clustering-significance-test

Permutation test for identification of statistically significant clusters in a phylogenetic tree

coverm

Read coverage calculator for metagenomics

crispropendb

deeplearningnotebooks

Tutorials for different deep learning models

download-and-reannotation-of-phage-genomes

A snakemake workflow for downloading and reannotating phage genomes

famsa

Algorithm for ultra-scale multiple sequence alignments (3M protein sequences in 5 minutes and 24 GB of RAM)

fastp

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

fluffy-racoon

Data visualisation scripts and notebooks for data-science projects

genomad-annotate-module

A snakemake workflow implementing the genomad annotate module steps

github-readme-quotes

🔥 Add Programming Quotes To Your GitHub Readme

handson-ml2

A series of Jupyter notebooks that walk you through the fundamentals of Machine Learning and Deep Learning in Python using Scikit-Learn, Keras and TensorFlow 2.

insilicoseq

:rocket: A sequencing simulator

jaeger

Jaeger is a quick and precise tool for detecting phages in sequence assemblies.

lib-rtf

Return time frequency based virus genotype clustering/detection program

machine-learning-articles

🧠💬 Articles I wrote about machine learning, archived from MachineCurve.com.

metaeuk

MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics

metagenome_assembly

metaphlan2

metawrap

MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis

mgnify-assembly-downloader

Downloads all assemblies available on MGnify

minced

Mining CRISPRs in Environmental Datasets

numpynet

Neural Networks library in pure numpy

phage-taxonomy