GenomicsAotearoa / environmental_metagenomics
A quick workflow to get researchers started with the bioinformatic pipeline used in the Environmental Metagenomics program.
☆10Updated 6 months ago
Related projects ⓘ
Alternatives and complementary repositories for environmental_metagenomics
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆24Updated 2 years ago
- Hybrid Assembler for Plasmids☆10Updated 2 years ago
- Structural and functional annotation of eukaryotic metagenome-assembled genomes☆21Updated last year
- pGWAS and functional filtering pipeline to identify candidate adaptive genetic traits in bacteria☆11Updated 6 years ago
- This is a comprehensive database for fast and accurately analyzing the phosphorus cycling genes.☆29Updated 2 years ago
- MAG Circularization Method☆33Updated 2 years ago
- Discover and annotate the virome☆31Updated last month
- Pipeline for metagenome and metatranscriptome joint assembly☆18Updated 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
- Please use mmgenome2 instead. Tools for extracting individual genomes from metagenomes☆27Updated 7 years ago
- SynTracker is a pipeline, designated to determine the biological relatedness of conspecific strains (microbial strains of the same specie…☆25Updated last week
- ZGA prokaryotic genome assembly and annotation pipeline☆11Updated 2 months ago
- Calculate assocations between genes and traits☆19Updated 3 weeks ago
- Genomewide Epistasis Analysis on Bacteria☆13Updated 2 months ago
- Tools for extracting individual genomes from metagenomes☆17Updated 11 months ago
- ☆12Updated 7 years ago
- ☆23Updated last year
- Assembly based core genome SNP alignments for bacteria☆25Updated 5 years ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆27Updated last year
- Reproducible scripts and notebooks for 2019 paper on population genetics in metagenomes☆15Updated 4 years ago
- ☆17Updated 2 months ago
- Extract metadata from biosamples in NCBI☆11Updated 3 years ago
- A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes☆17Updated last year
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes to select representatives for comparative genomics and met…☆40Updated 3 weeks ago
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆25Updated 3 weeks ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆19Updated 5 years ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆37Updated this week
- Bacterial taxonomy construction and evaluation in R☆13Updated 9 months ago
- Interactive, web tool for exploring pan-genome of bacterial strains☆45Updated last year