broadinstitute / StrainGELinks
strain-level analysis tools
☆38Updated 10 months ago
Alternatives and similar repositories for StrainGE
Users that are interested in StrainGE are comparing it to the libraries listed below
Sorting:
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.☆48Updated last week
- Automated strain separation of low-complexity metagenomes☆50Updated 3 years ago
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆58Updated last year
- Bacterial GWAS analysis☆43Updated last month
- Strain-level haplotyping for metagenomes with short or long-reads.☆52Updated 5 months ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆29Updated 2 years ago
- Discover and annotate the virome☆49Updated 2 weeks ago
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆41Updated 4 years ago
- Recombination-free trees☆60Updated 2 weeks ago
- Mandrake 🌿/👨🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding☆38Updated 6 months ago
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆25Updated last year
- MAGScoT - a MAG scoring and refinement tool☆36Updated 11 months ago
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆35Updated 4 months ago
- Strain Resolution ON Graphs☆47Updated 2 years ago
- Gene-flank analysis tool☆30Updated 9 months ago
- MAG Circularization Method☆32Updated 3 years ago
- ☆24Updated 7 months ago
- Phylogeny Enhanded Prediction of PAN-genome☆42Updated 5 years ago
- A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.☆30Updated last month
- A toolkit for prokaryotic comparative genomics☆50Updated 7 months ago
- Metagenomic Intra-Species Diversity Analysis (MIDAS)☆39Updated last year
- zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)☆62Updated last week
- Intra-species bacterial contamination detection☆25Updated 7 months ago
- a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome☆49Updated 2 years ago
- Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]☆41Updated 5 months ago
- Microbial agile accurate SNP Typer☆29Updated last year
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆38Updated 3 months ago
- Downstream processing of VAMB binning for Viral Elucidation☆50Updated last year
- frame-shift correction for long-read (meta)genomics☆33Updated last year
- 🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files☆24Updated 7 years ago