althonos / pysylph
PyO3 bindings and Python interface to sylph, an ultrafast method for containment ANI querying and taxonomic profiling.
☆17Updated 2 months ago
Alternatives and similar repositories for pysylph:
Users that are interested in pysylph are comparing it to the libraries listed below
- Fast implementation of KofamScan optimized for high-memory systems using PyHMMER☆11Updated 3 months ago
- PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.☆25Updated 2 months ago
- Plasmid analysis using rearrangement distances☆31Updated 3 months ago
- Genome size estimation from long read overlaps☆48Updated 2 months ago
- A Pyrodigal extension to predict genes in giant viruses and viruses with alternative genetic code.☆15Updated 6 months ago
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆22Updated 2 years ago
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes to select representatives for comparative genomics and met…☆43Updated last month
- alignment-free coverage calculation for metagenomic binning >100 times faster☆39Updated 2 months ago
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆22Updated 6 months ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆50Updated 7 months ago
- Classify metagenomic contigs as eukaryotic or prokaryotic☆32Updated last year
- Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]☆21Updated 2 months ago
- codoff: a program to measure the irregularity of the codon usage for a single genomic region (e.g. a BGC, phage, etc.) relative to the fu…☆11Updated 6 months ago
- A mathematically characterized hypothesis test for organism presence/absence in a metagenome☆30Updated 2 weeks ago
- Fast pairwise transmission inference from single genome and/or metagenomic data☆19Updated 4 months ago
- Comparison pipeline for Prokaryote Protein Coding Gene Predictors☆22Updated 9 months ago
- MetagenOmic read Re-Assigner and abundance quantifier☆18Updated 2 weeks ago
- software to identify primers that can distinguish genomes☆21Updated 3 weeks ago
- Visualize microbial evolution at the SNP level!☆14Updated 3 months ago
- Microbial agile accurate SNP Typer☆29Updated last year
- Hydrocarbon biodegradation gene annotation☆15Updated 2 years ago
- tool to determine optimal refrerence genome given a set of fasta files☆14Updated last year
- Python package to plot a phylogenetic tree on an existing matplotlib axis.☆15Updated last month
- MAGScoT - a MAG scoring and refinement tool☆31Updated 4 months ago
- This is graphanalyzer.py, a script designed to automatically interpret the outputs generated by vConTACT2 when using the INPHARED databas…☆18Updated last year
- TAXnomic Profile Aggregation and STAndardisation☆35Updated 3 months ago
- Mandrake 🌿/👨🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding☆36Updated this week
- A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes☆18Updated last year
- Python script to upload bins and MAGs to ENA (European Nucleotide Archive)☆23Updated 2 weeks ago