Lists (1)
Stars
GenSpectrum / LAPIS 8000
An API, a query engine, and a database schema for genomic sequences; currently with a focus on SARS-CoV-2
Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.
Genome modeling and design across all domains of life
MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets
A snakemake workflow for regions of difference discovery in Mycobacterium tuberculosis complex (MTBC) samples
High-quality circular representations of taxonomic and phylogenetic trees
Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, especially SARS-CoV-2
IRIDA and Galaxy deployment manifest definitions and scripts
Mathematical Modeling of Infectious Disease Dynamics
Machine Learning for Genomics and Therapeutics Resources (Cell Patterns)
Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
📦 🐳 Dockerfiles and documentation on tools for public health bioinformatics
A k-mer based program for the identification of known plasmids from whole-genome sequencing reads
A collection of sequencing protocols and bioinformatic resources for SARS-CoV-2 sequencing.
Real-time updates and information about key SARS-CoV-2 variants, plus the scripts that generate this information.
KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files
baltic - backronymed adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation. Development is back on the evogytis/baltic branch (i.e. here).
A tool for generating consensus long-read assemblies for bacterial genomes
Analysis of EBOV genome sequence from Guinea, Sierra Leone and Liberia from 2014-2016
Reviews for the Journal of Open Source Software