Hua Gao's starred repositories
zotero-better-bibtex
Make Zotero effective for us LaTeX holdouts
Polypolish
a short-read polishing tool for long-read assemblies
Deepbinner
a signal-level demultiplexer for Oxford Nanopore reads
viralrecon
Assembly and intrahost/low-frequency variant calling for viral samples
ClonalFrameML
ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
primalscheme
a tool for designing primer panels for multiplex PCR.
pangoLEARN
Store of the trained model for pangolin to access.
viral-pipelines
viral-ngs: complete pipelines
sra-human-scrubber
An SRA tool that takes as input local fastq file from a clinical infection sample, identifies and removes any significant human read, and outputs the edited (cleaned) fastq file that can safely be used for SRA submission.
public_health_viral_genomics
Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, especially SARS-CoV-2