LinXing Chen's repositories
PlasX
PlasX, a machine learning classifier for identifying plasmid sequences based on genetic architecture
vRhyme
Binning Virus Genomes from Metagenomes
PHIST
Phage-Host Interaction Search Tool
vpf-tools
Virus Protein Family tools
DomCycle
Identifying circular elements in complex microbial communities
ISEScan
A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome
Opfi
A Python package for discovery, annotation, and analysis of gene clusters in genomics or metagenomics data sets.
sra-tools
SRA Tools
Cenote-Taker2
Cenote-Taker2: Discover and Annotate Divergent Viral Contigs
metaMIC
Assessing and Improving the quality of metagenomic assemblies
BINF_toolkit
Handy scripts for routine bioinformatic analysis
spacegraphcats
Indexing large assembly graphs -- remember, in space, no one can hear you miao!
rawgraphs-app
A web interface to create custom vector-based visualizations on top of RAWGraphs core
temperate-phage-active-prophage-detection
detect temperate phage (active prophage) in assembled bacterial genome sequences
ncbitax2lin
🐞 Convert NCBI taxonomy dump into lineages
phirbo
Predict prokaryotic hosts for phage (meta) genomic sequences
clinker
Gene cluster comparison figure generator
Bandage
a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
kraken2
The second version of the Kraken taxonomic sequence classification system
CRISPRcasIdentifier
Machine learning for accurate identification and classification of CRISPR-Cas systems
PlasFlow
Software for prediction of plasmid sequences in metagenomic assemblies
GTDBTk
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.