raufs / skDERLinks
skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.
☆49Updated last month
Alternatives and similar repositories for skDER
Users that are interested in skDER are comparing it to the libraries listed below
Sorting:
- Calculate assocations between genes and traits☆28Updated 7 months ago
- Standalone Python re-implementation of the POLCA polisher from MaSuRCA☆40Updated 2 months ago
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆59Updated last year
- zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)☆64Updated last week
- Downstream processing of VAMB binning for Viral Elucidation☆50Updated last year
- Fast pairwise transmission inference from single genome and/or metagenomic data☆22Updated 3 months ago
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆35Updated 6 months ago
- Bacterial GWAS analysis☆45Updated last week
- alignment-free coverage calculation for metagenomic binning >100 times faster☆48Updated 7 months ago
- 🦠🧬🧑💻📇 Microbial genomes-to-report pipeline☆72Updated last month
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆31Updated last month
- A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.☆31Updated 3 months ago
- ☆24Updated 9 months ago
- A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes☆19Updated 2 years ago
- MDMcleaner the assessment, classification and refinement tool for microbial dark matter SAGs and MAGs☆23Updated 2 years ago
- Jaeger is a quick and precise tool for detecting phages in sequence assemblies.☆35Updated last week
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆29Updated 2 years ago
- EzAAI - High Throughput Prokaryotic AAI Calculator☆44Updated 3 months ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆55Updated 6 months ago
- Plasmid analysis using rearrangement distances☆46Updated last month
- RCandy: an R package for visualising homologous recombination events in bacterial genomes☆25Updated 3 years ago
- Recombination-free trees☆60Updated 2 months ago
- SCAPP is a plasmid assembly tool. This tool is described in our paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s4016…☆34Updated 2 years ago
- Gene Absence Presence Identification tool.☆27Updated 7 months ago
- Automated strain separation of low-complexity metagenomes☆51Updated 3 years ago
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆27Updated 3 years ago
- A toolkit for prokaryotic comparative genomics☆51Updated 2 weeks ago
- Workflow to assign Taxonomy to a bacteriophage genome isolate☆34Updated 7 months ago
- MetaGeneMark-2: Improved Gene Prediction in Metagenomes☆22Updated last year
- A workflow and scripts for large-scale antiSMASH analyses☆44Updated 6 months ago