hcdenbakker / sepiaLinks
taxonomic classifier based on the kraken2 algorithms and more
☆45Updated 2 months ago
Alternatives and similar repositories for sepia
Users that are interested in sepia are comparing it to the libraries listed below
Sorting:
- reference-based long read assemblies of bacterial genomes☆50Updated 4 years ago
- Split k-mer analysis – version 2☆87Updated 2 weeks ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆54Updated 2 years ago
- Fast k-mer based tool for multi locus sequence typing (MLST)☆46Updated 4 years ago
- Split Kmer Analysis☆65Updated 3 years ago
- Recombination-free trees☆59Updated 4 months ago
- A tool for removing redundant genomes from a set of assemblies☆73Updated last year
- Fast and space-efficient taxonomic classification of long reads☆43Updated 3 months ago
- a collection of scripts for organising bacterial genomes by species☆77Updated 3 years ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆60Updated last month
- TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomi…☆55Updated last month
- ☆36Updated 4 months ago
- LYVE-SET, a method of using hqSNPs to create a phylogeny, especially for outbreak investigations☆27Updated 11 months ago
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆42Updated 4 years ago
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆37Updated 2 months ago
- Get microbial sequence data easier and faster☆28Updated 5 years ago
- Strain resolver for metagenomics☆78Updated last year
- Predict MLST directly from uncorrected long reads☆27Updated 3 years ago
- Standalone Python re-implementation of the POLCA polisher from MaSuRCA☆37Updated 4 months ago
- Predict plasmids from uncorrected long read data☆40Updated 5 years ago
- A resistome profiler for Graphing Resistance Out Of meTagenomes☆66Updated 5 years ago
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆59Updated last year
- Interactive, web tool for exploring pan-genome of bacterial strains☆46Updated 2 years ago
- Gene-flank analysis tool☆28Updated 7 months ago
- This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye…☆59Updated 4 years ago
- Graph-based assembly phasing☆85Updated 3 months ago
- 🪡Correct and scaffold assemblies using long reads☆56Updated last year
- Automated strain separation of low-complexity metagenomes☆51Updated 3 years ago
- 🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files☆24Updated 7 years ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆52Updated 4 months ago