angelovangel / nxf-kraken2Links
A simple nextflow pipeline for running kraken2 and bracken in a docker container
☆20Updated 4 years 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☆42Updated 4 years ago
- Intra-species bacterial contamination detection☆25Updated 5 months ago
- Predict plasmids from uncorrected long read data☆40Updated 5 years ago
- Gene-flank analysis tool☆28Updated 7 months ago
- Interactive, web tool for exploring pan-genome of bacterial strains☆46Updated 2 years ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆26Updated 3 weeks ago
- Population analysis PIPEline 🛠🧬☆20Updated 3 months ago
- MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets☆29Updated last year
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆60Updated last month
- 🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files☆24Updated 7 years ago
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆26Updated 5 years ago
- Metagenomic Intra-Species Diversity Analysis (MIDAS)☆40Updated 11 months ago
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆36Updated 3 months ago
- strain-level analysis tools☆39Updated 9 months ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 4 years ago
- Microbiome classification pipeline☆66Updated 2 months ago
- Microbial agile accurate SNP Typer☆30Updated last year
- Identify phage regions in bacterial genomes for masking purposes☆34Updated 5 years ago
- whole genome MLST analysis☆46Updated last month
- Detection of NCLDV signatures in 'omic data☆35Updated last year
- 🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables☆28Updated last year
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆23Updated 2 years ago
- Collection of R scripts for SARS-CoV-2 (variant) analyses☆12Updated 2 years ago
- Bacterial GWAS analysis☆43Updated 3 weeks ago
- Recombination-free trees☆59Updated 4 months ago
- A pipeline for bioinformatics analysis of bacterial genomes☆30Updated last week
- reference-based long read assemblies of bacterial genomes☆50Updated 4 years ago
- Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data☆32Updated last week
- ☆18Updated 3 years ago
- Fast and space-efficient taxonomic classification of long reads☆43Updated 3 months ago