althonos / pysylphLinks
PyO3 bindings and Python interface to sylph, an ultrafast method for containment ANI querying and taxonomic profiling.
☆20Updated 11 months ago
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.☆27Updated 3 months ago
- Fast implementation of KofamScan optimized for high-memory systems using PyHMMER☆14Updated 3 months ago
- A Pyrodigal extension to predict genes in giant viruses and viruses with alternative genetic code.☆20Updated 2 weeks ago
- Python package to plot a phylogenetic tree on an existing matplotlib axis.☆26Updated 4 months ago
- Comparison pipeline for Prokaryote Protein Coding Gene Predictors☆26Updated 3 weeks ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆59Updated 7 months ago
- software to identify primers that can distinguish genomes☆20Updated 2 weeks 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
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆59Updated 2 years ago
- Phylogenetic maximum representation sampling: choosing most representative strains or taxa☆40Updated 2 months ago
- Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)☆39Updated last year
- Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.☆23Updated last month
- ☆52Updated 7 months ago
- alignment-free coverage calculation for metagenomic binning >100 times faster☆48Updated 8 months ago
- Mandrake 🌿/👨🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding☆39Updated 9 months ago
- 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
- Python package to obtain, parse and explore biological taxonomies (GTDB, NCBI, Silva, Greengenes, OTT)☆47Updated 5 months ago
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆25Updated last year
- Resolving Species Level Classification Using Emu☆14Updated last year
- Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]☆43Updated 8 months ago
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆24Updated 2 years ago
- A tool in order to accurately remove primer sequences from NGS reads in an amplicon experiment☆20Updated 3 weeks ago
- Miscellaneous Perl scripts from 20 years in microbial bioinformatics☆17Updated last year
- Remove human reads from a sequencing run☆45Updated last week
- Basecalling configuration prediction through FASTQ files☆32Updated 2 weeks ago
- Fast pairwise transmission inference from single genome and/or metagenomic data☆22Updated 4 months ago
- Non-redundant pangenome assemblies from multiple genomes or bins☆14Updated 6 months ago
- ViromeQC is a computational tool to benchmark and quantify non-viral contamination in VLP-enrihed viromes. ViromeQC provides an enrichmen…☆20Updated 3 years ago
- ☆24Updated 10 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