angelovangel / nxf-kraken2Links
A simple nextflow pipeline for running kraken2 and bracken in a docker container
☆20Updated last month
Alternatives and similar repositories for nxf-kraken2
Users that are interested in nxf-kraken2 are comparing it to the libraries listed below
Sorting:
- Population analysis PIPEline 🛠🧬☆22Updated 7 months ago
- Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data☆45Updated last month
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆29Updated 2 years ago
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆42Updated 4 years ago
- ⚡️🧬 FastMLST: A multi-core tool for multilocus sequence typing of draft genome assemblies☆27Updated last week
- Interactive, web tool for exploring pan-genome of bacterial strains☆48Updated 2 years ago
- Microbial agile accurate SNP Typer☆29Updated last year
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆25Updated 6 years ago
- Intra-species bacterial contamination detection☆25Updated 9 months ago
- strain-level analysis tools☆39Updated last year
- Metagenomic Intra-Species Diversity Analysis (MIDAS)☆39Updated last year
- Pipeline for metagenome and metatranscriptome joint assembly☆21Updated 2 years ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆28Updated 4 months ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆64Updated 5 months ago
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆35Updated 7 months ago
- A pipeline for bioinformatics analysis of bacterial genomes☆31Updated this week
- Visualisation application for Klebsiella genotypes generated by Kleborate.☆10Updated 2 months ago
- MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets☆31Updated last year
- Bacterial GWAS analysis☆46Updated last month
- Predict plasmids from uncorrected long read data☆41Updated last month
- Gene-flank analysis tool☆33Updated 11 months ago
- ☆14Updated 4 years ago
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆59Updated 2 years ago
- Repository for scripts and resources used for metagenomics with Nanopore, PacBio and Illumina sequencing☆21Updated 2 years ago
- Strain-level abundances estimation in metagenomic samples using variation graphs☆24Updated 2 years ago
- Phylogeny Enhanded Prediction of PAN-genome☆43Updated 5 years ago
- Fast and space-efficient taxonomic classification of long reads☆43Updated 3 months ago
- Bacterial genomes finishing tool for structural insights on draft genomes☆23Updated 2 years ago
- Detection of NCLDV signatures in 'omic data☆35Updated last year
- Recombination-free trees☆60Updated 2 months ago