rki-mf1 / clean
A nextflow pipeline for decontamination of short reads, long reads and contigs
☆44Updated 4 months ago
Alternatives and similar repositories for clean
Users that are interested in clean are comparing it to the libraries listed below
Sorting:
- Fast k-mer based tool for multi locus sequence typing (MLST)☆44Updated 4 years ago
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆26Updated 5 years ago
- A toolkit for prokaryotic comparative genomics☆49Updated 3 months ago
- Repository for scripts and resources used for metagenomics with Nanopore, PacBio and Illumina sequencing☆21Updated 2 years ago
- SHOOT.bio - the phylogenetic search engine☆24Updated last year
- Bacterial GWAS analysis☆40Updated 3 weeks ago
- MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets☆29Updated 10 months ago
- Split Kmer Analysis☆64Updated 2 years ago
- HoCoRT - Remove specific organisms from sequencing reads☆17Updated 4 months ago
- Gene-flank analysis tool☆27Updated 4 months ago
- Recombination-free trees☆58Updated last month
- reference-based long read assemblies of bacterial genomes☆49Updated 3 years ago
- de.NBI Nanopore Training Course☆20Updated 2 years ago
- Inferring bacterial recombination rates from large-scale sequencing datasets.☆42Updated 2 years ago
- OPAL: Open-community Profiling Assessment tooL☆28Updated 4 months ago
- A small bash script that automates sweeping Guppy parameters in an attempt to optimise basecalling rate☆30Updated 3 years ago
- PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.☆58Updated last year
- Phylogeny Enhanded Prediction of PAN-genome☆40Updated 4 years ago
- PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples☆45Updated last year
- BEAV: Bacterial Element Annotation reVamped☆65Updated 6 months ago
- Pangenome analysis of eukaryotes.☆18Updated 4 years ago
- GTDB taxonomy taxdump files with trackable TaxIds☆53Updated 2 weeks ago
- Automated strain separation of low-complexity metagenomes☆51Updated 3 years ago
- SpydrPick: mutual information based detection of pairs of genomic loci co-evolving under a shared selective pressure.☆13Updated 3 years ago
- whole genome MLST analysis☆42Updated last month
- Identify short variants and structural variants from raw sequencing data or genomic sequences☆25Updated last year
- Metagenomics-related extended functionalities to samtools☆21Updated last year
- An R package designed for drawing gene arrow maps☆77Updated 3 weeks ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆53Updated 2 years ago
- A pipeline for performing genome-wide association tests for bacterial genomes.☆27Updated 7 years ago