raufs / skDER
skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes to select representatives for comparative genomics and metagenomics.
☆43Updated last week
Alternatives and similar repositories for skDER:
Users that are interested in skDER are comparing it to the libraries listed below
- Calculate assocations between genes and traits☆23Updated 4 months ago
- Bacterial GWAS analysis☆36Updated this week
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆27Updated last year
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆26Updated 4 months ago
- PlasX, a machine learning classifier for identifying plasmid sequences based on genetic architecture☆32Updated 3 years ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆50Updated 7 months ago
- MAGScoT - a MAG scoring and refinement tool☆31Updated 4 months ago
- Microbial agile accurate SNP Typer☆29Updated last year
- Prophage Activity Estimator☆26Updated 9 months ago
- ☆25Updated last year
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆34Updated last week
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆22Updated 7 months ago
- Jaeger is a quick and precise tool for detecting phages in sequence assemblies.☆25Updated 3 months ago
- Structural and functional annotation of eukaryotic metagenome-assembled genomes☆22Updated last year
- SCAPP is a plasmid assembly tool. This tool is described in our paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s4016…☆31Updated 2 years ago
- Pipeline for metagenome and metatranscriptome joint assembly☆20Updated 2 years ago
- A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes☆18Updated last year
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆25Updated 2 years ago
- aweMAGs: a fully automated workflow for eukariotic MAGs☆11Updated last year
- Downstream processing of VAMB binning for Viral Elucidation☆48Updated 8 months ago
- ☆20Updated 5 months ago
- EzAAI - High Throughput Prokaryotic AAI Calculator☆38Updated 4 months ago
- Discover and annotate the virome☆37Updated 4 months ago
- MAG Circularization Method☆33Updated 2 years ago
- Fast pairwise transmission inference from single genome and/or metagenomic data☆19Updated 5 months ago
- Unified Human Gut Virome Catalog☆27Updated 7 months ago
- Plasmid analysis using rearrangement distances☆31Updated 3 months ago
- Identify phage regions in bacterial genomes for masking purposes☆30Updated 5 years ago
- Identify and remove contaminants from metagenome-assembled genomes☆18Updated last year
- SynTracker is a pipeline, designated to determine the biological relatedness of conspecific strains (microbial strains of the same specie…☆26Updated last month