broadinstitute / StrainGELinks
strain-level analysis tools
☆37Updated 7 months ago
Alternatives and similar repositories for StrainGE
Users that are interested in StrainGE are comparing it to the libraries listed below
Sorting:
- Bacterial GWAS analysis☆40Updated last week
- Strain-level haplotyping for metagenomes with short or long-reads.☆51Updated last month
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆24Updated 10 months ago
- MAG Circularization Method☆33Updated 3 years ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆59Updated 3 months ago
- MAGScoT - a MAG scoring and refinement tool☆35Updated 7 months ago
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆26Updated 5 years ago
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆27Updated 7 months ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆28Updated last year
- Calculate assocations between genes and traits☆23Updated 2 months ago
- Gene-flank analysis tool☆27Updated 5 months ago
- Genome size estimation from long read overlaps☆56Updated last month
- A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.☆25Updated last month
- ☆21Updated 4 months ago
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.☆45Updated last week
- ☆16Updated 4 years ago
- A mathematically characterized hypothesis test for organism presence/absence in a metagenome☆30Updated 2 weeks ago
- Microbial agile accurate SNP Typer☆29Updated last year
- A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes☆19Updated 2 years ago
- 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
- SynTracker is a pipeline, designated to determine the biological relatedness of conspecific strains (microbial strains of the same specie…☆29Updated 4 months ago
- Recombination-free trees☆58Updated 2 months ago
- Strain Resolution ON Graphs☆47Updated last year
- Strain-level abundances estimation in metagenomic samples using variation graphs☆25Updated 2 years ago
- 🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files☆24Updated 7 years ago
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆23Updated 2 years ago
- Assembly based core genome SNP alignments for bacteria☆25Updated 5 years ago
- ViromeQC is a computational tool to benchmark and quantify non-viral contamination in VLP-enrihed viromes. ViromeQC provides an enrichmen…☆19Updated 2 years ago
- Discover and annotate the virome☆42Updated last month
- Detect contigs of complete circular genomes☆23Updated 5 years ago