Pinned Repositories
AnHyDeg
Database of anaerobic hydrocarbon degradation genes used for functional gene searching of metagenome data sets
BamM
Metagenomics-focused BAM file manipulation
BioData
All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")
bioscripts
some useful scripts for working with genomics and sequencing data
ClonalFrameML
ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
cmseq
Set of utilities on sequences and BAM files
CRISPRDetect_3.0
EBAME18
Long read metagenomics practical at EBAME18
emg-viral-pipeline
VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies
EukRep
Thexiyang's Repositories
Thexiyang/emg-viral-pipeline
VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies
Thexiyang/bioscripts
some useful scripts for working with genomics and sequencing data
Thexiyang/ClonalFrameML
ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
Thexiyang/cmseq
Set of utilities on sequences and BAM files
Thexiyang/CRISPRDetect_3.0
Thexiyang/EBAME18
Long read metagenomics practical at EBAME18
Thexiyang/FeGenie
HMM-based identification and categorization of iron genes and iron gene operons in genomes and metagenomes
Thexiyang/graftM
GraftM - Rapid community profiles from metagenomes
Thexiyang/gRodon
Thexiyang/GToTree
A user-friendly workflow for phylogenomics
Thexiyang/hAMRonization
Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure
Thexiyang/HGTector
HGTector2: Genome-wide prediction of horizontal gene transfer based on distribution of sequence homology patterns.
Thexiyang/MagicCave
A platform for targeted annotation of (meta)genomic and (meta)transcriptomic datasets using HMM sets.
Thexiyang/maliampi
Maximum Likelihood Amplicon Pipeline
Thexiyang/mcorr
Inferring bacterial recombination rates from large-scale sequencing datasets.
Thexiyang/METABOLIC
A scalable high-throughput metabolic and biogeochemical functional trait profiler
Thexiyang/metagenomics_crash_course
Thexiyang/metapop
A pipeline for the macro- and micro-diversity analyses and visualization of metagenomic-derived populations
Thexiyang/MIDAS
An integrated pipeline for estimating strain-level genomic variation from metagenomic data
Thexiyang/MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
Thexiyang/pgap
NCBI Prokaryotic Genome Annotation Pipeline
Thexiyang/prokka
:zap: :aquarius: Rapid prokaryotic genome annotation
Thexiyang/RefineM
A toolbox for improving metagenome-assembled genomes.
Thexiyang/samsa2
SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customizable reference databases.
Thexiyang/shovill
Faster SPAdes assembly of Illumina reads
Thexiyang/singlem
De-novo OTUs from shotgun metagenomes
Thexiyang/SqueezeMeta
A complete pipeline for metagenomic analysis
Thexiyang/vamb
Variational autoencoder for metagenomic binning
Thexiyang/VirusDiscoveryProject
Software, architecture, and data index design for the 2018/2019 Virus Discovery Project
Thexiyang/woltka
Web of Life Toolkit App