Yasas1994

Jaeger

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

Clustering-significance-test

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

ICTV-TaxonomyChallenge

phables

🫧🧬 From fragmented assemblies to high-quality bacteriophage genomes

bioconda-recipes

Conda recipes for the bioconda channel.

phage_contig_annotator

Annotates genes on putative phage contigs with protein orthologous groups using PHROGs

DeepLearningNoteBooks

Tutorials for different deep learning models

MGnify-assembly-downloader

Downloads all assemblies available on MGnify

download-and-reannotation-of-phage-genomes

A snakemake workflow for downloading and reannotating phage genomes

genomad-annotate-module

A snakemake workflow implementing the genomad annotate module steps

atlas

ATLAS - Three commands to start analyzing your metagenome data

SqueezeMeta

A complete pipeline for metagenomic analysis

CAT

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

CoverM

Read coverage calculator for metagenomics

github-readme-quotes

🔥 Add Programming Quotes To Your GitHub Readme

viroinf-hiddensee

Datasets for the ViroInf Hiddensee workshop

Phage-taxonomy

metagenome_assembly

sequence_fragment_simulator

metaWRAP

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

What_the_Phage

WtP: Phage identification via nextflow and docker or singularity

fastp

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

awesome-go

A curated list of awesome Go frameworks, libraries and software

FAMSA

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

pharokka

fast phage annotation program

metaeuk

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

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.

pyhmmer

Cython bindings and Python interface to HMMER3.

machine-learning-articles

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

fluffy-racoon

Data visualisation scripts and notebooks for data-science projects