hcdenbakker / sepia
taxonomic classifier based on the kraken2 algorithms and more
☆45Updated 3 years ago
Alternatives and similar repositories for sepia:
Users that are interested in sepia are comparing it to the libraries listed below
- Fast k-mer based tool for multi locus sequence typing (MLST)☆44Updated 4 years ago
- Split Kmer Analysis☆63Updated 2 years ago
- Recombination-free trees☆58Updated last month
- reference-based long read assemblies of bacterial genomes☆48Updated 3 years ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆53Updated last year
- Full-length de novo viral haplotype reconstruction from noisy long reads☆18Updated last year
- Automated strain separation of low-complexity metagenomes☆51Updated 3 years ago
- ☆35Updated 2 weeks ago
- Calculate confidence scores from Kraken2 output☆22Updated last year
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆59Updated last month
- Strain-level haplotyping for metagenomes with short or long-reads.☆50Updated 2 weeks ago
- LYVE-SET, a method of using hqSNPs to create a phylogeny, especially for outbreak investigations☆26Updated 8 months ago
- Remove human reads from a sequencing run☆40Updated 6 months ago
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆41Updated 4 years ago
- Fast and space-efficient taxonomic classification of long reads☆43Updated 2 months ago
- a collection of scripts for organising bacterial genomes by species☆76Updated 3 years ago
- whole genome MLST analysis☆41Updated last month
- ☆52Updated 3 years ago
- Strain resolver for metagenomics☆73Updated 8 months ago
- Precise host read removal☆94Updated last week
- A tool for removing redundant genomes from a set of assemblies☆71Updated last year
- in silico typing of the H. influenzae cap locus☆12Updated 9 months ago
- Kraken(2) database based on the GTDB project☆27Updated 6 years ago
- A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing☆70Updated 3 years ago
- Bifrost graph gene caller.☆93Updated 7 months ago
- TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomi…☆34Updated this week
- Predict MLST directly from uncorrected long reads☆27Updated 3 years ago
- Identify phage regions in bacterial genomes for masking purposes☆30Updated 5 years ago
- Split k-mer analysis – version 2☆82Updated 2 months ago
- Get microbial sequence data easier and faster☆28Updated 5 years ago