LinXing Chen's repositories
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
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.
Jorg
MAG Circularization Method
nanopore_script
A snakemake assembly pipeline for hybrid metagenome sequencing
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
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