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Starred repositories
Databases for wg/cgMLST analysis with the PN2.0 software
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Updated Sep 11, 2024
jcw349 / nextclade_data
Forked from nextstrain/nextclade_dataDatasets for https://github.com/nextstrain/nextclade
This repository contains the source code for the datasets used in the implementation of the dengue lineage system in NextClade. The organizational workflow was developed based on the workflow creat…
app to collapse Pango lineages for reporting
An open-source software package to power microbial genomic databases
An open-source pathogen sequence database dedicated to equitable sharing, transparent governance, & empowering global public health.
Quickly search, compare, and analyze genomic and metagenomic data sets.
Mercury prepares and formats metadata for submission to national & international genomic databases.
Consensus sequences for U.S. H5N1 clade 2.3.4.4b
Influenza data pipeline to automate genotyping assignment
Fast, scalable, accurate and accessible Bayesian phylogenetics
StxTyper uses a standardized algorithm to accurately type both known and unknown Shiga toxin operons from assembled genomic sequence.
Repository containing a method for automatically identifying pathogen lineages from a phylogeny.
a tool for designing primer panels for multiplex PCR.
Workflows and scripts for the assembly and analysis of SARS-CoV-2 whole genome tiled amplicon sequencing.
assign sequencing reads to influenza A serotypes
Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.
ncezid-biome / AlleleCodes
Forked from gmaniscoo/AlleleCodesPython script(s) for assigning allele codes under current PulseNet nomenclature system in BioNumerics but as a command-line executable without BioNumerics dependencies
In-silico PCR, primer design and padlock design for in-situ sequencing
Shell script used to run the ARTIC minion pipeline to analyze amplicon sequencing data generated using the pan-DENV primers sequenced on ONT platforms
Nextflow pipeline for the analysis of Hantavirus (and related) genomes generated using amplicon-based approaches
Scripts and reference files to type Group A Streptococcus