LinXing Chen's repositories
MMseqs2
MMseqs2: ultra fast and sensitive search and clustering suite
DRAM
Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
chainsaw
Rapidly Search and Hunt through Windows Forensic Artefacts
fastp
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
MGnifyR
R package for searching, downloading and analysis of EBI MGnify metagenomics data
bioconda-recipes
Conda recipes for the bioconda channel.
sphae
NEW!!! Phage annotations and predictions. A spae is a prediction or foretelling. We'll foretell you what your phage is doing!
astra
pyHMMer-based sequence search and retrieval tool.
defense-finder
Systematic search of all known anti-phage systems.
prodigal-gv
A fork of Prodigal meant to improve gene calling for giant viruses and viruses that use alternative genetic codes
umap
Uniform Manifold Approximation and Projection
foldseek
Foldseek enables fast and sensitive comparisons of large structure sets.
ViWrap
A wrapper to identify, bin, classify, and predict host-viral relationship for viruses
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
vsearch
Versatile open-source tool for microbiome analysis
Complete-Python-3-Bootcamp
Course Files for Complete Python 3 Bootcamp Course on Udemy
PlasmidHunter
This tool predicts plasmid sequences from genomic and metagenomic assemblies using machine learning.
PhaGCN_newICTV
Update model for ICTV2022
genomad
geNomad: Identification of mobile genetic elements
phamb
Downstream processing of VAMB binning for Viral Elucidation
FriendsDontLetFriends
Friends don't let friends make certain types of data visualization - What are they and why are they bad.
nanopore_script
A snakemake assembly pipeline for hybrid metagenome sequencing
Jorg
MAG Circularization Method
PlasX
PlasX, a machine learning classifier for identifying plasmid sequences based on genetic architecture