althonos / pyskaniLinks
PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.
☆27Updated 3 months ago
Alternatives and similar repositories for pyskani
Users that are interested in pyskani are comparing it to the libraries listed below
Sorting:
- PyO3 bindings and Python interface to sylph, an ultrafast method for containment ANI querying and taxonomic profiling.☆20Updated 11 months ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆59Updated 7 months ago
- Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)☆39Updated last year
- software to identify primers that can distinguish genomes☆20Updated 2 weeks ago
- Comparison pipeline for Prokaryote Protein Coding Gene Predictors☆26Updated 3 weeks ago
- Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.☆23Updated last month
- Fast implementation of KofamScan optimized for high-memory systems using PyHMMER☆14Updated 3 months ago
- Non-redundant pangenome assemblies from multiple genomes or bins☆14Updated 6 months ago
- Microbial agile accurate SNP Typer☆29Updated last year
- ☆10Updated 6 months ago
- Computation of average nucleotide identity with the use of MMseqs2☆15Updated 11 months ago
- Fast pairwise transmission inference from single genome and/or metagenomic data☆22Updated 4 months ago
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆59Updated 2 years ago
- Python package to plot a phylogenetic tree on an existing matplotlib axis.☆26Updated 4 months ago
- codoff: a program to measure the irregularity of the codon usage for a single genomic region (e.g. a BGC, prophage, etc.) relative to the…☆13Updated 3 weeks ago
- Genome size estimation from long read overlaps☆74Updated last week
- The Whole Genome Sequencing Coverage Plot (wgscovplot) is a tool to generate HTML Interactive Coverage Plot given coverage depth informat…☆19Updated last year
- snapper☆13Updated last year
- HyLight is a strain aware de novo assembly method based on the overlap-layout-consensus (OLC) paradigm that leverages the strengths of NG…☆12Updated last year
- A pipeline based on EMU, a taxonomic profiler optimized for long 16S rRNA reads.☆16Updated this week
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆24Updated 2 years ago
- ⚡️🧬 FastMLST: A multi-core tool for multilocus sequence typing of draft genome assemblies☆27Updated 3 weeks ago
- Finding regions of similarity between plasmids☆16Updated 3 years ago
- A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.☆31Updated 4 months ago
- Automated strain separation of low-complexity metagenomes☆53Updated 4 years ago
- ☆24Updated 10 months ago
- A mathematically characterized hypothesis test for organism presence/absence in a metagenome☆33Updated this week
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Updated 7 years ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆29Updated 2 years ago
- Assort phage protein sequences into phamilies using MMseqs2☆11Updated 11 months ago