alexcritschristoph / soil_popgen
Reproducible scripts and notebooks for 2019 paper on population genetics in metagenomes
☆15Updated 4 years ago
Related projects ⓘ
Alternatives and complementary repositories for soil_popgen
- Population genomics from metagenomes☆11Updated 2 months ago
- Structural and functional annotation of eukaryotic metagenome-assembled genomes☆21Updated last year
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes to select representatives for comparative genomics and met…☆40Updated 3 weeks ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆27Updated last year
- SCAPP is a plasmid assembly tool. This tool is described in our paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s4016…☆28Updated last year
- PlasX, a machine learning classifier for identifying plasmid sequences based on genetic architecture☆29Updated 2 years ago
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆24Updated 2 years ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆19Updated 5 years ago
- ☆23Updated last year
- Download NCBI assembly genomes with ftp. rsync, ascp☆11Updated 2 years ago
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆22Updated 4 months ago
- pGWAS and functional filtering pipeline to identify candidate adaptive genetic traits in bacteria☆11Updated 6 years ago
- Pipeline for metagenome and metatranscriptome joint assembly☆18Updated last year
- Prophage Activity Estimator☆26Updated 5 months ago
- Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).☆24Updated 7 months ago
- Downstream processing of VAMB binning for Viral Elucidation☆46Updated 4 months ago
- Pathway Tools multiprocessing wrapper (for PathoLogic).☆15Updated 7 months ago
- A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes☆17Updated last year
- MAGScoT - a MAG scoring and refinement tool☆28Updated last month
- Set of utilities on sequences and BAM files☆25Updated 3 years ago
- ☆12Updated 7 years ago
- Quality control plotting for long reads☆10Updated 6 months ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆41Updated 4 months ago
- ☆14Updated last week
- Interactive, web tool for exploring pan-genome of bacterial strains☆45Updated last year
- SynTracker is a pipeline, designated to determine the biological relatedness of conspecific strains (microbial strains of the same specie…☆25Updated last week
- MAG Circularization Method☆33Updated 2 years ago
- Genomewide Epistasis Analysis on Bacteria☆13Updated 2 months ago
- ☆14Updated last year
- RCandy: an R package for visualising homologous recombination events in bacterial genomes☆18Updated 2 years ago