jolespin / pykofamsearchLinks
Fast implementation of KofamScan optimized for high-memory systems using PyHMMER
☆11Updated 6 months ago
Alternatives and similar repositories for pykofamsearch
Users that are interested in pykofamsearch are comparing it to the libraries listed below
Sorting:
- 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 2 months ago
- PyO3 bindings and Python interface to sylph, an ultrafast method for containment ANI querying and taxonomic profiling.☆18Updated 5 months ago
- PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.☆27Updated 3 weeks ago
- Python package to plot a phylogenetic tree on an existing matplotlib axis.☆22Updated 2 months ago
- software to identify primers that can distinguish genomes☆21Updated 4 months ago
- Python implementation of barrnap (Bacterial ribosomal RNA predictor)☆20Updated 4 months ago
- A mathematically characterized hypothesis test for organism presence/absence in a metagenome☆30Updated 2 weeks ago
- ☆10Updated 3 weeks ago
- ☆21Updated 4 months 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 last year
- Comparison pipeline for Prokaryote Protein Coding Gene Predictors☆23Updated this week
- Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]☆33Updated 2 months ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Updated 6 years ago
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.☆45Updated last week
- Finding regions of similarity between plasmids☆16Updated 2 years ago
- Visualize microbial evolution at the SNP level!☆14Updated 3 weeks ago
- Microbial agile accurate SNP Typer☆29Updated last year
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆24Updated 10 months ago
- Utility to analyse a group of closely related MAgs/Genomes/bins/SUBs of more or less dubious origin☆15Updated 8 months ago
- tool to determine optimal refrerence genome given a set of fasta files☆15Updated 2 years ago
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆23Updated 2 years ago
- A Pyrodigal extension to predict genes in giant viruses and viruses with alternative genetic code.☆17Updated 9 months ago
- Bacterial GWAS analysis☆40Updated last week
- A new high-resolution long-read metagenome assembler for even noisy reads☆61Updated last week
- Identify and remove contaminants from metagenome-assembled genomes☆18Updated last year
- Computation of average nucleotide identity with the use of MMseqs2☆13Updated 5 months ago
- Genome size estimation from long read overlaps☆56Updated last month
- ☆11Updated 2 weeks ago
- ViromeQC is a computational tool to benchmark and quantify non-viral contamination in VLP-enrihed viromes. ViromeQC provides an enrichmen…☆19Updated 2 years ago
- Targeted Detection and Reconstruction of Plasmids☆20Updated last year