nf-core / pathogensurveillanceLinks
Surveillance of pathogens using population genomics and sequencing
☆24Updated this week
Alternatives and similar repositories for pathogensurveillance
Users that are interested in pathogensurveillance are comparing it to the libraries listed below
Sorting:
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆26Updated 5 years ago
- Plot genome alignment figure using progressiveMauve & genoPlotR☆22Updated 2 years ago
- BACTpipe: An assembly and annotation pipeline for bacterial genomics☆20Updated 6 months ago
- Genome size estimation from long read overlaps☆56Updated last month
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆28Updated last year
- A pipeline for performing genome-wide association tests for bacterial genomes.☆27Updated 7 years ago
- MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets☆29Updated 11 months ago
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆24Updated 10 months ago
- ⚡️🧬 FastMLST: A multi-core tool for multilocus sequence typing of draft genome assemblies☆24Updated 3 months ago
- Visualisation application for Klebsiella genotypes generated by Kleborate.☆9Updated 4 years ago
- Remove human reads from a sequencing run☆40Updated 8 months ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆20Updated 6 years ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆25Updated 8 months ago
- ZGA prokaryotic genome assembly and annotation pipeline☆12Updated 8 months ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆59Updated 3 months ago
- k-mer based Pipeline to identify the Serotype from Illumina NGS reads☆23Updated last year
- Assembly based core genome SNP alignments for bacteria☆25Updated 5 years ago
- Mandrake 🌿/👨🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding☆38Updated 2 months ago
- ☆26Updated last year
- Bacterial GWAS analysis☆40Updated last week
- Interactive, web tool for exploring pan-genome of bacterial strains☆45Updated 2 years ago
- Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).☆26Updated last year
- Population analysis PIPEline 🛠🧬☆18Updated last month
- Dadaist2 🟨 Highway to R☆13Updated 2 months ago
- A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxon to identify (and remove) is Homo sapiens. Remo…☆20Updated this week
- Read contamination removal☆25Updated last year
- Comparison pipeline for Prokaryote Protein Coding Gene Predictors☆23Updated this week
- A pipeline for bioinformatics analysis of bacterial genomes☆29Updated 3 weeks ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Updated 6 years ago
- pipeline for read mapping, snp calling and annotation for bacterial genomes☆12Updated last year