pirovc / multitaxLinks
Python package to obtain, parse and explore biological taxonomies (GTDB, NCBI, Silva, Greengenes, OTT)
☆44Updated last week
Alternatives and similar repositories for multitax
Users that are interested in multitax are comparing it to the libraries listed below
Sorting:
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆59Updated last year
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆23Updated 2 years ago
- Scalable creating/updating of metagenome profiling databases☆61Updated 3 weeks ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆52Updated 3 months ago
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆42Updated 4 years ago
- strain-level analysis tools☆38Updated 8 months ago
- TAXnomic Profile Aggregation and STAndardisation☆41Updated 8 months ago
- Strain-level abundances estimation in metagenomic samples using variation graphs☆25Updated 2 years ago
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆26Updated 5 years ago
- Fast and space-efficient taxonomic classification of long reads☆43Updated 2 months ago
- Recombination-free trees☆58Updated 3 months ago
- Automated strain separation of low-complexity metagenomes☆51Updated 3 years ago
- An SRA tool that takes as input local fastq file from a clinical infection sample, identifies and removes any significant human read, and…☆48Updated last year
- Interactive, web tool for exploring pan-genome of bacterial strains☆46Updated 2 years ago
- MAGScoT - a MAG scoring and refinement tool☆35Updated 9 months ago
- Mandrake 🌿/👨🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding☆38Updated 4 months ago
- Strain Resolution ON Graphs☆48Updated 2 years ago
- Better and faster Rust implementation of the FragGeneScan gene prediction model for short and error-prone reads.☆26Updated 5 months ago
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆38Updated last month
- Assembly based core genome SNP alignments for bacteria☆25Updated 5 years ago
- Automatic eukaryotic taxonomic classification☆29Updated 2 months ago
- A containerized bioinformatics pipeline for viral metagenomic data analysis☆32Updated 11 months ago
- Extract lineage CSVs from NCBI for use with sourmash lca.☆29Updated last year
- Kraken(2) database based on the GTDB project☆27Updated 6 years ago
- PARTIE is a program to partition sequence read archive (SRA) metagenomics data into amplicon and shotgun data sets. The user-supplied ann …☆26Updated 2 years ago
- Get microbial sequence data easier and faster☆28Updated 5 years ago
- A package to annotate protein sequences☆59Updated 4 months ago
- Non-redundant pangenome assemblies from multiple genomes or bins☆13Updated 2 months ago
- frame-shift correction for long-read (meta)genomics☆34Updated last year
- Phasing for metagenomics using PacBio long reads☆17Updated 4 years ago