Hua-clearlabs's Stars
rrwick/Trycycler
A tool for generating consensus long-read assemblies for bacterial genomes
tseemann/abricate
:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes
tseemann/mlst
:id: Scan contig files against PubMLST typing schemes
ncbi/amr
AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.
davidemms/OrthoFinder
Phylogenetic orthology inference for comparative genomics
nextstrain/augur
Pipeline components for real-time phylodynamic analysis
neherlab/treetime
Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction
paulstothard/cgview
CGView is a Java package for generating high-quality, zoomable maps of circular genomes.
marbl/Krona
Interactively explore metagenomes and more from a web browser.
ncbi/rapt
Read Assembly and Annotation Pipeline Tool
ncbi/pgap
NCBI Prokaryotic Genome Annotation Pipeline
ncbi/SKESA
SKESA assembler
tseemann/nullarbor
:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology
fbreitwieser/pavian
🌈 Interactive analysis of metagenomics data
CDCgov/MicrobeTrace
The Visualization Multitool for Molecular Epidemiology and Bioinformatics
nextstrain/nextclade_data
Datasets for https://github.com/nextstrain/nextclade
lenaschimmel/sc2rf
SARS-Cov-2 Recombinant Finder for fasta sequences
cov-lineages/pango-designation
Repository for suggesting new lineages that should be added to the current scheme