danielpodlesny / samestr
SameStr identifies shared strains between pairs of metagenomic samples based on the similarity of SNV profiles.
☆17Updated 5 months ago
Alternatives and similar repositories for samestr:
Users that are interested in samestr are comparing it to the libraries listed below
- MetaSNV, a metagenomic SNV calling pipeline.☆20Updated 2 years ago
- ☆16Updated 4 years ago
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆34Updated last week
- SCAPP is a plasmid assembly tool. This tool is described in our paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s4016…☆31Updated 2 years ago
- Microbial agile accurate SNP Typer☆29Updated last year
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes to select representatives for comparative genomics and met…☆43Updated last week
- Phasing for metagenomics using PacBio long reads☆17Updated 3 years ago
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆22Updated 2 years ago
- SynTracker is a pipeline, designated to determine the biological relatedness of conspecific strains (microbial strains of the same specie…☆26Updated last month
- A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.☆24Updated last week
- ViromeQC is a computational tool to benchmark and quantify non-viral contamination in VLP-enrihed viromes. ViromeQC provides an enrichmen…☆18Updated 2 years ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆27Updated last year
- MAG Circularization Method☆33Updated 2 years ago
- Calculate assocations between genes and traits☆23Updated 4 months ago
- viralFlye pipeline☆18Updated 6 months ago
- Set of utilities on sequences and BAM files☆26Updated 3 years ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆50Updated 7 months ago
- MAGScoT - a MAG scoring and refinement tool☆31Updated 4 months ago
- Detection of NCLDV signatures in 'omic data☆33Updated 7 months ago
- Bacterial GWAS analysis☆36Updated this week
- Gene-flank analysis tool☆27Updated 2 months ago
- Downstream processing of VAMB binning for Viral Elucidation☆48Updated 8 months ago
- Code used to analyse and plot metadata of metagenomic binning tools☆12Updated 6 months ago
- Unified Human Gut Virome Catalog☆27Updated 7 months ago
- Fast and space-efficient taxonomic classification of long reads☆43Updated this week
- ☆31Updated last year
- A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes☆18Updated last year
- TAXnomic Profile Aggregation and STAndardisation☆35Updated 4 months ago
- Pipeline for metagenome and metatranscriptome joint assembly☆20Updated 2 years ago
- Discover and annotate the virome☆37Updated 4 months ago