jolespin / pykofamsearch
Fast implementation of KofamScan optimized for high-memory systems using PyHMMER
☆11Updated 4 months ago
Alternatives and similar repositories for pykofamsearch:
Users that are interested in pykofamsearch are comparing it to the libraries listed below
- 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 8 months ago
- PyO3 bindings and Python interface to sylph, an ultrafast method for containment ANI querying and taxonomic profiling.☆18Updated 3 months ago
- PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.☆27Updated 3 weeks ago
- Python implementation of barrnap (Bacterial ribosomal RNA predictor)☆17Updated 2 months ago
- ☆11Updated 2 months ago
- Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]☆22Updated 4 months ago
- A mathematically characterized hypothesis test for organism presence/absence in a metagenome☆30Updated 2 weeks ago
- Computation of average nucleotide identity with the use of MMseqs2☆13Updated 3 months ago
- software to identify primers that can distinguish genomes☆21Updated 2 months ago
- Comparison pipeline for Prokaryote Protein Coding Gene Predictors☆23Updated 11 months ago
- A Pyrodigal extension to predict genes in giant viruses and viruses with alternative genetic code.☆17Updated 7 months ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Updated 6 years ago
- Map query sequences to the assemblies of all pre-June 2023 bacteria (https://ftp.ebi.ac.uk/pub/databases/AllTheBacteria/Releases/0.2/) on…☆12Updated 10 months ago
- MetagenOmic read Re-Assigner and abundance quantifier☆18Updated 2 months ago
- StrainXpress is a de novo assembly method which base on overlap-layout-consensus (OLC) paradigm and can fast and accurately assemble high…☆13Updated last year
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆22Updated 2 years ago
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆23Updated 8 months ago
- Visualize microbial evolution at the SNP level!☆14Updated 4 months ago
- Targeted Detection and Reconstruction of Plasmids☆20Updated 10 months ago
- ccfind - circular complete genome finder with clues of terminal redundancy☆15Updated 4 years ago
- alignment-free coverage calculation for metagenomic binning >100 times faster☆39Updated 2 weeks ago
- Classify metagenomic contigs as eukaryotic or prokaryotic☆33Updated 2 years ago
- Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.☆22Updated 3 weeks ago
- viralFlye pipeline☆18Updated 7 months ago
- Utility to analyse a group of closely related MAgs/Genomes/bins/SUBs of more or less dubious origin☆14Updated 6 months ago
- From genomes to phenotypes: Traitar3, the microbial trait analyzer (for Python3)☆22Updated 8 months ago
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.☆44Updated 3 weeks ago
- ViromeQC is a computational tool to benchmark and quantify non-viral contamination in VLP-enrihed viromes. ViromeQC provides an enrichmen…☆18Updated 2 years ago
- Identify and remove contaminants from metagenome-assembled genomes☆18Updated last year
- Microbial agile accurate SNP Typer☆29Updated last year