althonos / pysylph
PyO3 bindings and Python interface to sylph, an ultrafast method for containment ANI querying and taxonomic profiling.
☆16Updated last week
Related projects ⓘ
Alternatives and complementary repositories for pysylph
- Strain-level haplotyping for metagenomes with short or long-reads.☆40Updated 4 months ago
- PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.☆23Updated last week
- Plasmid analysis using rearrangement distances☆29Updated 2 months ago
- Targeted Detection and Reconstruction of Plasmids☆19Updated 6 months ago
- Fast implementation of KofamScan optimized for high-memory systems using PyHmmer☆11Updated this week
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes to select representatives for comparative genomics and met…☆40Updated 2 weeks ago
- A mathematically characterized hypothesis test for organism presence/absence in a metagenome☆30Updated this week
- A pipeline for bioinformatics analysis of bacterial genomes☆19Updated 4 months ago
- ☆10Updated last year
- Comparison pipeline for Prokaryote Protein Coding Gene Predictors☆22Updated 6 months ago
- Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]☆19Updated 8 months ago
- alignment-free coverage calculation for metagenomic binning >100 times faster☆37Updated 2 months ago
- MAGScoT - a MAG scoring and refinement tool☆28Updated last month
- Bacterial GWAS analysis☆32Updated last month
- software to identify primers that can distinguish genomes☆20Updated last week
- MetagenOmic read Re-Assigner and abundance quantifier☆17Updated 4 months ago
- Python implementation of barrnap (Bacterial ribosomal RNA predictor)☆13Updated 2 months ago
- Intra-species bacterial contamination detection☆22Updated last year
- Calculate assocations between genes and traits☆19Updated 2 weeks ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆37Updated 2 months ago
- tool to determine optimal refrerence genome given a set of fasta files☆14Updated last year
- A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes☆17Updated last year
- ccfind - circular complete genome finder with clues of terminal redundancy☆15Updated 4 years ago
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆22Updated 3 months ago
- Non-redundant pangenome assemblies from multiple genomes or bins☆13Updated 3 months ago
- Microbial agile accurate SNP Typer☆29Updated 10 months ago
- Finding regions of similarity between plasmids☆16Updated 2 years ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Updated 6 years ago
- ☆23Updated 8 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…☆10Updated 3 months ago