yibo dong's repositories
alphafold
Open source code for AlphaFold.
amr
AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.
artic-ncov2019
ARTIC nanopore protocol for nCoV2019 novel coronavirus
bactopia
A flexible pipeline for complete analysis of bacterial genomes
bakta
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
bioconda-recipes
Conda recipes for the bioconda channel.
csvtk
A cross-platform, efficient and practical CSV/TSV toolkit in Golang
docker-builds
:package: :whale: Dockerfiles and documentation on tools for public health bioinformatics
esm
Evolutionary Scale Modeling (esm): Pretrained language models for proteins
FastANI
Fast Whole-Genome Similarity (ANI) Estimation
figtree
Automatically exported from code.google.com/p/figtree
Freyja
Depth-weighted De-Mixing
gubbins
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
iqtree2
NEW location of IQ-TREE software for efficient phylogenomic software by maximum likelihood http://www.iqtree.org
KrakenTools
KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files
LongQC
LongQC is a tool for the data quality control of the PacBio and ONT long reads.
MicrobeTrace
The Visualization Multitool for Molecular Epidemiology and Bioinformatics
mycosnp-nf
only CDCgov/mycosnp-nf-1.4 works in HPG
pbbioconda
PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
pfaster
pneumococcal FASTA serotype calling
pipeline-resources
Bioinformatics Pipeline and Visualization resources
ProteinLM
Protein Language Model
ProtTrans
ProtTrans is providing state of the art pretrained language models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using Transformers Models.
public_health_bioinformatics
Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health concern.
pytablewriter
pytablewriter is a Python library to write a table in various formats: AsciiDoc / CSV / Elasticsearch / HTML / JavaScript / JSON / LaTeX / LDJSON / LTSV / Markdown / MediaWiki / NumPy / Excel / Pandas / Python / reStructuredText / SQLite / TOML / TSV.
SARS-CoV-2
SARs-CoV-2 Primer schemes
staphb_toolkit
Python Toolkit for using containerized programs in either Singularity or Docker
tower-cli
Nextflow Tower CLI tool (beta)
training
Nextflow training material