jordanlab / STingLinks
Ultrafast sequence typing and gene detection from NGS raw reads
☆20Updated 4 years ago
Alternatives and similar repositories for STing
Users that are interested in STing are comparing it to the libraries listed below
Sorting:
- Strain-level abundances estimation in metagenomic samples using variation graphs☆24Updated 2 years ago
- ☆14Updated 4 years ago
- Read contamination removal☆25Updated last year
- Influenza genome analysis Nextflow workflow☆23Updated last month
- BACTpipe: An assembly and annotation pipeline for bacterial genomics☆20Updated 10 months ago
- De novo VIral Genome Annotator☆23Updated last year
- screening metagenomes for arbitrary lineages, using gene-centric assembly methods and phylogenetics☆11Updated 5 years ago
- Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data☆12Updated last year
- Get microbial sequence data easier and faster☆28Updated 5 years ago
- A simple nextflow pipeline for running kraken2 and bracken in a docker container☆20Updated 3 weeks ago
- ☆26Updated 2 years ago
- Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens☆32Updated 2 weeks ago
- Bioinformatics pipeline for nanopore sequencing data☆11Updated 6 years ago
- tool to determine optimal refrerence genome given a set of fasta files☆15Updated 2 years ago
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆25Updated 6 years ago
- Plot genome alignment figure using progressiveMauve & genoPlotR☆22Updated 3 years ago
- Output FASTQ summary statistics in JSON format☆29Updated 3 years ago
- Prokaryotic Pangenome Analysis☆24Updated 3 years ago
- Mandrake 🌿/👨🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding☆38Updated 7 months ago
- Genomic neighbor typing of bacterial pathogens using MinHash☆43Updated 2 years ago
- A streamlined workflow and GUI for real-time species identification and pathogen characterization via nanopore sequencing data. Engineere…☆18Updated last year
- Interactive, web tool for exploring pan-genome of bacterial strains☆48Updated 2 years ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆29Updated 2 years ago
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆22Updated 2 years ago
- k-mer based Pipeline to identify the Serotype from Illumina NGS reads☆25Updated 2 years ago
- A nextflow version of the Wochenende reference metagenome binning and visualization pipeline☆15Updated 10 months ago
- MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets☆30Updated last year
- A simple-to-use tool for visualizing and comparing genome contexts for numerous genomes☆17Updated last year
- TADA - Targeted Amplicon Diversity Analysis - a DADA2-focused Nextflow workflow for any targeted amplicon region☆22Updated this week
- Intra-species bacterial contamination detection☆25Updated 8 months ago