linxingchen

cobra

A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during de novo assembly.

noveltree

NovelTree is a highly parallelized and computationally efficient phylogenomic workflow that infers gene families, gene family trees, species trees, and gene family evolutionary history.

prodigal-gv

A fork of Prodigal meant to improve gene calling for giant viruses and viruses that use alternative genetic codes

astra

pyHMMer-based sequence search and retrieval tool.

bioconda-recipes

Conda recipes for the bioconda channel.

Carter-and-Olm-Cell-2023---db-info

README for Zenodo archive associated with publication Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Gut Microbes

Complete-Python-3-Bootcamp

Course Files for Complete Python 3 Bootcamp Course on Udemy

contig-extender

defense-finder

Systematic search of all known anti-phage systems.

DomCycle

Identifying circular elements in complex microbial communities

foldseek

Foldseek enables fast and sensitive comparisons of large structure sets.

FriendsDontLetFriends

Friends don't let friends make certain types of data visualization - What are they and why are they bad.

genomad

geNomad: Identification of mobile genetic elements

Jorg

MAG Circularization Method

MobMess

nanopore_script

A snakemake assembly pipeline for hybrid metagenome sequencing

PhaGCN2.0

PhaGCN_newICTV

Update model for ICTV2022

phamb

Downstream processing of VAMB binning for Viral Elucidation

PHIST

Phage-Host Interaction Search Tool

PlasmidHunter

This tool predicts plasmid sequences from genomic and metagenomic assemblies using machine learning.

PlasX

PlasX, a machine learning classifier for identifying plasmid sequences based on genetic architecture

plsdbapi

pprodigal

Python3 wrapper for parallelized gene prediction using Prodigal

sphae

NEW!!! Phage annotations and predictions. A spae is a prediction or foretelling. We'll foretell you what your phage is doing!

umap

Uniform Manifold Approximation and Projection

ViWrap

A wrapper to identify, bin, classify, and predict host-viral relationship for viruses

vpf-tools

Virus Protein Family tools

vRhyme

Binning Virus Genomes from Metagenomes

vsearch

Versatile open-source tool for microbiome analysis