genomic-surveillance
There are 0 repository under genomic-surveillance topic.
tomwenseleers / LineageExplorer
Estimate growth rate advantage of SARS-CoV2 variants of concern based on international genomic surveillance data and multinomial spline fits
Language:R 24sanjaynagi / rna-seq-pop
Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data
Language:Jupyter Notebook 17- viper
alex-ranieri / viper
VIPER is a user-friendly software for assembling and identifying viral genomes (currently SARS-CoV-2, Dengue, and Influenza), from Illumina sequencing data generated through genomic surveillance.
Language:Shell 4 PandemicPreventionInstitute / NGS-Capacity-map
Since May 2021 the PPI Data & Analytics team has been cleaning, analyzing, and visualizing data from GISAID, FIND, WHO, and Our World In Data. In collaboration with the team at FIND we have developed a series of maps that describe next-generation sequencing capacity. The main outputs were code, data repositories, and visualizations that appear on the FIND page here along with an in-depth explanation of the methodology.
Language:Jupyter Notebook 3rki-mf1 / MpoxRadar
MpoxRadar frontend codebase: an interactive dashboard for genomic surveillance of MPXV.
Language:Python 2STTLab / HIV-64148
HIV-64148, an integration of multiple long-read genome assemblers with a pipeline for analysis of HIV-1 genomic data from Oxford Nanopore Sequencing Technology or PacBio Real-Time (SMRT) Sequencing technology.
Language:Python 1AMarinhoSN / RGFbackend
Backend routines for genomic surveillance data processing of Rede Genomica Fiocruz
Language:Python 0A state-of-the-art snakemake workflow for amplicon sequencing
Language:Jupyter Notebook 0CDCgov / bpertussis-ciwgs
Culture-Independent Whole Genome Sequencing (CIWGS) Read Filter Pipeline 🧪🧬🖥️
Language:Nextflow