alexcritschristoph / soil_popgenLinks
Reproducible scripts and notebooks for 2019 paper on population genetics in metagenomes
☆16Updated 5 years ago
Alternatives and similar repositories for soil_popgen
Users that are interested in soil_popgen are comparing it to the libraries listed below
Sorting:
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆28Updated last year
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆25Updated 2 years ago
- Structural and functional annotation of eukaryotic metagenome-assembled genomes☆22Updated 2 years ago
- ZGA prokaryotic genome assembly and annotation pipeline☆12Updated 8 months ago
- pGWAS and functional filtering pipeline to identify candidate adaptive genetic traits in bacteria☆11Updated 7 years ago
- Download NCBI assembly genomes with ftp. rsync, ascp☆10Updated 2 years ago
- Population genomics from metagenomes☆11Updated 9 months ago
- Set of utilities on sequences and BAM files☆27Updated 3 years ago
- Small and simple scripts useful for various bioinformatics purposes e.g. extract sequences from fasta files☆20Updated 2 years ago
- Find Prokaryotic DNA methylase genes in proteins, contigs, or genomes☆11Updated 11 months ago
- SynTracker is a pipeline, designated to determine the biological relatedness of conspecific strains (microbial strains of the same specie…☆29Updated 4 months ago
- Pipeline for metagenome and metatranscriptome joint assembly☆21Updated 2 years ago
- PlasX, a machine learning classifier for identifying plasmid sequences based on genetic architecture☆34Updated 3 years ago
- Calculate assocations between genes and traits☆23Updated 2 months ago
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆24Updated 10 months ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆20Updated 6 years ago
- ☆18Updated 3 years ago
- Prophage Activity Estimator☆26Updated last year
- ☆25Updated last year
- SCAPP is a plasmid assembly tool. This tool is described in our paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s4016…☆30Updated 2 years ago
- MAG Circularization Method☆33Updated 3 years ago
- Interactive, web tool for exploring pan-genome of bacterial strains☆45Updated 2 years ago
- Trans-Kingdom Marker Gene Pipeline for Taxonomic Profiling of Human Metagenomes☆19Updated last year
- MetaGeneMark-2: Improved Gene Prediction in Metagenomes☆21Updated last year
- IslandPath standalone software☆32Updated last year
- Genome-wide gene gain/loss mapping tool using DTL(Duplication-Transfer-Loss) reconciliation method☆15Updated 2 years ago
- Quality control plotting for long reads☆10Updated last year
- A Swiss-Army-Knife for Bioinformaticians☆12Updated 3 weeks ago
- Bacterial GWAS analysis☆40Updated last week
- Pathway Tools multiprocessing wrapper (for PathoLogic).☆14Updated 2 months ago