angelovangel / nxf-kraken2
A simple nextflow pipeline for running kraken2 and bracken in a docker container
☆20Updated 3 years ago
Alternatives and similar repositories for nxf-kraken2:
Users that are interested in nxf-kraken2 are comparing it to the libraries listed below
- Predict plasmids from uncorrected long read data☆39Updated 5 years ago
- Get microbial sequence data easier and faster☆28Updated 5 years ago
- Intra-species bacterial contamination detection☆24Updated 2 months ago
- Interactive, web tool for exploring pan-genome of bacterial strains☆45Updated 2 years ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆55Updated last week
- Gene-flank analysis tool☆26Updated last month
- Gene Absence Presence Identification tool.☆26Updated last year
- Influenza genome analysis Nextflow workflow☆24Updated 3 weeks ago
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆34Updated last week
- k-mer based Pipeline to identify the Serotype from Illumina NGS reads☆21Updated last year
- MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets☆28Updated 6 months ago
- Influenza genome analysis Nextflow workflow☆19Updated last week
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆40Updated 4 years ago
- 🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables☆27Updated last year
- Identify phage regions in bacterial genomes for masking purposes☆30Updated 5 years ago
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆30Updated last month
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆26Updated 5 years ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆24Updated 3 months ago
- Ley Lab MetaGenome Profiler DataBase generator☆48Updated 2 years ago
- IslandPath standalone software☆31Updated last year
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 3 years ago
- 🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files☆23Updated 6 years ago
- whole genome MLST analysis☆40Updated 8 months ago
- TAXnomic Profile Aggregation and STAndardisation☆34Updated 3 months ago
- ⚡️🧬 FastMLST: A multi-core tool for multilocus sequence typing of draft genome assemblies☆23Updated last year
- ☆27Updated last year
- Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data☆23Updated last year
- ☆36Updated 2 years ago
- Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).☆24Updated 9 months ago
- Strain Resolution ON Graphs☆47Updated last year