angelovangel / nxf-kraken2Links
A simple nextflow pipeline for running kraken2 and bracken in a docker container
☆20Updated 3 months ago
Alternatives and similar repositories for nxf-kraken2
Users that are interested in nxf-kraken2 are comparing it to the libraries listed below
Sorting:
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆43Updated 5 years ago
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆35Updated 8 months ago
- Gene-flank analysis tool☆34Updated last year
- MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets☆33Updated last year
- Microbial agile accurate SNP Typer☆30Updated 2 years ago
- Interactive, web tool for exploring pan-genome of bacterial strains☆48Updated 3 years ago
- Intra-species bacterial contamination detection☆25Updated 10 months ago
- Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data☆48Updated 3 weeks ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆28Updated 5 months ago
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆24Updated 6 years ago
- Strain Resolution ON Graphs☆49Updated 2 years ago
- Miscellaneous Perl scripts from 20 years in microbial bioinformatics☆18Updated last year
- strain-level analysis tools☆39Updated last year
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆21Updated 6 years ago
- Predict plasmids from uncorrected long read data☆41Updated 2 months ago
- Automated strain separation of low-complexity metagenomes☆52Updated 4 years ago
- Order and orientation of complete bacterial genomes☆29Updated 6 months ago
- Microbiome classification pipeline☆65Updated 7 months ago
- Population analysis PIPEline 🛠🧬☆22Updated this week
- A pipeline for bioinformatics analysis of bacterial genomes☆32Updated this week
- Phylogeny Enhanded Prediction of PAN-genome☆43Updated 5 years ago
- 🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files☆24Updated 7 years ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆29Updated 2 years ago
- Metagenomic Intra-Species Diversity Analysis (MIDAS)☆41Updated last year
- Repository for scripts and resources used for metagenomics with Nanopore, PacBio and Illumina sequencing☆21Updated 2 years ago
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆27Updated 3 years ago
- k-mer based Pipeline to identify the Serotype from Illumina NGS reads☆25Updated 2 years ago
- Bacterial GWAS analysis☆46Updated 2 months ago
- ☆14Updated 4 years ago
- Lemur is a tool for rapid and accurate taxonomic profiling on long-read metagenomic datasets☆25Updated 5 months ago