hcdenbakker / sepiaLinks
taxonomic classifier based on the kraken2 algorithms and more
☆45Updated 6 months ago
Alternatives and similar repositories for sepia
Users that are interested in sepia are comparing it to the libraries listed below
Sorting:
- CRyPTIC data processing pipelines☆34Updated last year
- reference-based long read assemblies of bacterial genomes☆51Updated 4 years ago
- Fast k-mer based tool for multi locus sequence typing (MLST)☆45Updated 5 years ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆54Updated 2 years ago
- Split Kmer Analysis☆65Updated 3 years ago
- Split k-mer analysis – version 2☆101Updated last month
- Recombination-free trees☆62Updated 3 months ago
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆42Updated 5 years ago
- a collection of scripts for organising bacterial genomes by species☆81Updated 3 years ago
- Full-length de novo viral haplotype reconstruction from noisy long reads☆21Updated 2 years ago
- Gene-flank analysis tool☆34Updated 11 months ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆59Updated 8 months ago
- Remove human reads from a sequencing run☆45Updated last week
- A tool for removing redundant genomes from a set of assemblies☆77Updated 3 months ago
- TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomi…☆60Updated 2 weeks ago
- ☆36Updated 8 months ago
- LYVE-SET, a method of using hqSNPs to create a phylogeny, especially for outbreak investigations☆27Updated last year
- A resistome profiler for Graphing Resistance Out Of meTagenomes☆65Updated 5 years ago
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆25Updated 6 years ago
- Automated strain separation of low-complexity metagenomes☆53Updated 4 years ago
- Get microbial sequence data easier and faster☆28Updated 6 years ago
- Improve the quality of a denovo assembly by scaffolding and gap filling☆57Updated 4 years ago
- Kraken(2) database based on the GTDB project☆28Updated 6 years ago
- This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye…☆58Updated 4 years ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆64Updated 5 months ago
- Predict plasmids from uncorrected long read data☆41Updated last month
- Pipeline to generate NGS reads from a phylogeny☆39Updated 3 years ago
- Fast and space-efficient taxonomic classification of long reads☆43Updated 3 months ago
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆59Updated 2 years ago
- tools for assessing the accuracy of genome assemblies☆35Updated last year