yibo dong's repositories
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.
esm
Evolutionary Scale Modeling (esm): Pretrained language models for proteins
LongQC
LongQC is a tool for the data quality control of the PacBio and ONT long reads.
bakta
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
KrakenTools
KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files
csvtk
A cross-platform, efficient and practical CSV/TSV toolkit in Golang
mycosnp-nf
only CDCgov/mycosnp-nf-1.4 works in HPG
MicrobeTrace
The Visualization Multitool for Molecular Epidemiology and Bioinformatics
FastANI
Fast Whole-Genome Similarity (ANI) Estimation
alphafold
Open source code for AlphaFold.
Freyja
Depth-weighted De-Mixing
tower-cli
Nextflow Tower CLI tool (beta)
training
Nextflow training material
amr
AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.
iqtree2
NEW location of IQ-TREE software for efficient phylogenomic software by maximum likelihood http://www.iqtree.org
public_health_bioinformatics
Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health concern.
bactopia
A flexible pipeline for complete analysis of bacterial genomes
docker-builds
:package: :whale: Dockerfiles and documentation on tools for public health bioinformatics
pipeline-resources
Bioinformatics Pipeline and Visualization resources
gubbins
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
pbbioconda
PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
SARS-CoV-2
SARs-CoV-2 Primer schemes
staphb_toolkit
Python Toolkit for using containerized programs in either Singularity or Docker
artic-ncov2019
ARTIC nanopore protocol for nCoV2019 novel coronavirus
pfaster
pneumococcal FASTA serotype calling
NCHHSTP-DTBE-Varpipe-WGS
This repository contains an analysis pipeline developed to characterize WGS output
BMGAP
The Bacterial Meningitis Genome Analysis Platform, an analysis pipeline, ExpressJS API, and ReactJS webapp for the analysis and characterization of bacterial meningitis samples