nf-core / pathogensurveillanceLinks
Surveillance of pathogens using population genomics and sequencing
☆28Updated last week
Alternatives and similar repositories for pathogensurveillance
Users that are interested in pathogensurveillance are comparing it to the libraries listed below
Sorting:
- Tutorial for bacterial GWAS pipline and bugwas, created for Bodega Bay 2016 NGS workshop☆18Updated 9 years ago
- k-mer based Pipeline to identify the Serotype from Illumina NGS reads☆24Updated last year
- BACTpipe: An assembly and annotation pipeline for bacterial genomics☆20Updated 6 months ago
- A pipeline for performing genome-wide association tests for bacterial genomes.☆27Updated 7 years ago
- TAXnomic Profile Aggregation and STAndardisation☆41Updated 7 months ago
- Assembly based core genome SNP alignments for bacteria☆25Updated 5 years ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆28Updated 2 years ago
- A method of assessing sequence complexity based on kmer frequencies☆32Updated 7 years ago
- MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets☆29Updated 11 months ago
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆26Updated 5 years ago
- Intra-species bacterial contamination detection☆25Updated 4 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 2 weeks ago
- Read contamination removal☆25Updated last year
- Trimming tool for Oxford Nanopore sequence data☆21Updated 4 years ago
- Find Unique genomic Regions☆30Updated 2 months ago
- Strain-level abundances estimation in metagenomic samples using variation graphs☆25Updated 2 years ago
- Mandrake 🌿/👨🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding☆38Updated 3 months ago
- Get microbial sequence data easier and faster☆28Updated 5 years ago
- Influenza genome analysis Nextflow workflow☆22Updated 2 months ago
- Horizontal Gene Transfer Detection by Mapping Sequencing Reads☆21Updated 7 years ago
- ☆26Updated last year
- Strain Prediction and Analysis with Representative SEquence☆19Updated 6 months ago
- a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome☆49Updated 2 years ago
- Interactive, web tool for exploring pan-genome of bacterial strains☆45Updated 2 years ago
- Gene-flank analysis tool☆27Updated 6 months ago
- Genome size estimation from long read overlaps☆57Updated 2 months ago
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆24Updated 11 months ago
- SpydrPick: mutual information based detection of pairs of genomic loci co-evolving under a shared selective pressure.☆13Updated 3 years ago
- Output FASTQ summary statistics in JSON format☆30Updated 2 years ago
- ZGA prokaryotic genome assembly and annotation pipeline☆12Updated 9 months ago