althonos / pysylphLinks
PyO3 bindings and Python interface to sylph, an ultrafast method for containment ANI querying and taxonomic profiling.
☆20Updated last year
Alternatives and similar repositories for pysylph
Users that are interested in pysylph are comparing it to the libraries listed below
Sorting:
- PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.☆28Updated 4 months ago
- Fast implementation of KofamScan optimized for high-memory systems using PyHMMER☆14Updated 4 months ago
- Python package to plot a phylogenetic tree on an existing matplotlib axis.☆27Updated 5 months ago
- A Pyrodigal extension to predict genes in giant viruses and viruses with alternative genetic code.☆20Updated last month
- software to identify primers that can distinguish genomes☆20Updated 2 weeks ago
- Comparison pipeline for Prokaryote Protein Coding Gene Predictors☆26Updated 2 months ago
- Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)☆39Updated 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
- Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.☆23Updated 2 months ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆63Updated 9 months ago
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆59Updated 2 years ago
- Mandrake 🌿/👨🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding☆39Updated 10 months ago
- Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]☆44Updated 9 months ago
- Non-redundant pangenome assemblies from multiple genomes or bins☆14Updated 7 months ago
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆24Updated 2 years ago
- alignment-free coverage calculation for metagenomic binning >100 times faster☆48Updated 9 months ago
- Genome size estimation from long read overlaps☆80Updated last month
- Fast and space-efficient taxonomic classification of long reads☆42Updated 4 months ago
- tool to determine optimal refrerence genome given a set of fasta files☆15Updated 2 years ago
- Computation of average nucleotide identity with the use of MMseqs2☆15Updated last year
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆25Updated last year
- Meteor is a plateform for quantitative metagenomics profiling of complex ecosystems. Meteor relies on genes catalogue to perform species-…☆32Updated 3 weeks ago
- Manipulate and generate figures for trees in Newick format☆22Updated 5 months ago
- Finding regions of similarity between plasmids☆16Updated 3 years ago
- Genomic neighbor typing of bacterial pathogens using MinHash☆42Updated 3 years ago
- Phylogenetic maximum representation sampling: choosing most representative strains or taxa☆40Updated 3 months ago
- A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.☆35Updated last year
- Python implementation of barrnap (Bacterial ribosomal RNA predictor)☆23Updated 11 months ago
- The Whole Genome Sequencing Coverage Plot (wgscovplot) is a tool to generate HTML Interactive Coverage Plot given coverage depth informat…☆19Updated last year
- Microbial agile accurate SNP Typer☆30Updated 2 years ago