unipept / umgap
A taxonomic classifier for shotgun metagenomics reads
☆12Updated this week
Alternatives and similar repositories for umgap:
Users that are interested in umgap are comparing it to the libraries listed below
- MetagenOmic read Re-Assigner and abundance quantifier☆18Updated 2 months ago
- Strain-level abundances estimation in metagenomic samples using variation graphs☆25Updated 2 years ago
- PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.☆27Updated 3 weeks ago
- k-mers and the like☆21Updated 2 weeks ago
- A k-mer-based maximum likelihood method for estimating distances of reads to genomes and phylogenetic placement.☆10Updated 2 weeks ago
- Embedding-based indexing for compact storage, rapid querying, and curation of bacterial pan-genomes☆10Updated this week
- software to identify primers that can distinguish genomes☆21Updated 2 months ago
- Map query sequences to the assemblies of all pre-June 2023 bacteria (https://ftp.ebi.ac.uk/pub/databases/AllTheBacteria/Releases/0.2/) on…☆12Updated 10 months ago
- Non-redundant pangenome assemblies from multiple genomes or bins☆13Updated last month
- StrainXpress is a de novo assembly method which base on overlap-layout-consensus (OLC) paradigm and can fast and accurately assemble high…☆13Updated last year
- Prediction of microbial interactions in complex communities☆12Updated 7 months ago
- Raspir, the rare species identifier☆11Updated last year
- Highly sensitive pathogen detection☆12Updated 4 years ago
- Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA alignment☆16Updated 6 years ago
- MetaSNV, a metagenomic SNV calling pipeline.☆20Updated 3 years ago
- MiCoP is a method for high-accuracy profiling of viral and fungal metagenomic communities.☆15Updated 3 years ago
- Compute a pairwise SNP distance matrix from one or two alignment(s)☆24Updated 6 months ago
- fast, multithreaded sourmash operations: search, compare, and gather.☆22Updated this week
- Given a set of kmers (fasta format) and a set of sequences (fasta format), this tool will extract the sequences containing the kmers.☆21Updated last year
- metagenome population recombination rate estimation pipeline☆12Updated this week
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆22Updated 2 years ago
- Systematic resistome analysis☆10Updated 5 years ago
- Protologgger is a tool for the description of novel taxa by providing taxonomic, functional and ecological insights☆14Updated last year
- Pipeline to evaluate pangenomes, e.g. from the variation it contains or how well reads map☆10Updated 3 years ago
- kASA - k-Mer Analysis of Sequences based on Amino acid-like encoding☆23Updated last year
- Protocols, data and code associated with the MK-SpikeSeq method for quantifying the absolute abundances of microbiota samples☆13Updated 3 years ago
- A Hierarchical Approach to Pangenomics Inference☆11Updated 11 months ago
- De novo metagenome assembler☆13Updated 2 years ago
- Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.☆22Updated 3 weeks ago
- Lowest Common Ancestor from a SAM/BAM/CRAM alignment file☆9Updated 7 months ago