jolespin / pykofamsearchLinks
Fast implementation of KofamScan optimized for high-memory systems using PyHMMER
☆14Updated 2 weeks ago
Alternatives and similar repositories for pykofamsearch
Users that are interested in pykofamsearch are comparing it to the libraries listed below
Sorting:
- PyO3 bindings and Python interface to sylph, an ultrafast method for containment ANI querying and taxonomic profiling.☆20Updated 9 months ago
- Python package to plot a phylogenetic tree on an existing matplotlib axis.☆24Updated last month
- ☆24Updated 7 months ago
- PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.☆26Updated 3 weeks ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆52Updated 5 months ago
- Comparison pipeline for Prokaryote Protein Coding Gene Predictors☆25Updated last month
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.☆48Updated last week
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆58Updated last year
- Microbial agile accurate SNP Typer☆29Updated last year
- A Pyrodigal extension to predict genes in giant viruses and viruses with alternative genetic code.☆18Updated last month
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆25Updated last year
- alignment-free coverage calculation for metagenomic binning >100 times faster☆46Updated 6 months ago
- A mathematically characterized hypothesis test for organism presence/absence in a metagenome☆31Updated 2 weeks ago
- Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]☆41Updated 5 months ago
- Standalone Python re-implementation of the POLCA polisher from MaSuRCA☆39Updated 3 weeks ago
- Genome size estimation from long read overlaps☆60Updated 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 this week
- Bacterial GWAS analysis☆43Updated last month
- RabbitTClust: enabling fast clustering analysis of millions bacteria genomes with MinHash sketches☆49Updated last month
- Computation of average nucleotide identity with the use of MMseqs2☆15Updated 9 months ago
- Fast pairwise transmission inference from single genome and/or metagenomic data☆21Updated last month
- Automated strain separation of low-complexity metagenomes☆50Updated 3 years ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆29Updated 2 years ago
- Plasmid analysis using rearrangement distances☆45Updated 2 weeks ago
- Colinear block visualisation tool☆31Updated last year
- A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.☆34Updated 9 months ago
- Classify metagenomic contigs as eukaryotic or prokaryotic☆39Updated 2 years ago
- Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)☆37Updated last year
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆22Updated 2 years ago
- Miscellaneous Perl scripts from 20 years in microbial bioinformatics☆17Updated last year