xbiome / StrainPanDA
A method for reconstruction of subspecies composition and functional profiles from metagenomic data
☆13Updated 10 months ago
Alternatives and similar repositories for StrainPanDA:
Users that are interested in StrainPanDA are comparing it to the libraries listed below
- Strain-level abundances estimation in metagenomic samples using variation graphs☆25Updated 2 years ago
- StrainXpress is a de novo assembly method which base on overlap-layout-consensus (OLC) paradigm and can fast and accurately assemble high…☆13Updated last year
- MetaSNV, a metagenomic SNV calling pipeline.☆20Updated 3 years ago
- MiCoP is a method for high-accuracy profiling of viral and fungal metagenomic communities.☆15Updated 2 years ago
- strain-level analysis tools☆35Updated 5 months ago
- kASA - k-Mer Analysis of Sequences based on Amino acid-like encoding☆23Updated last year
- MetagenOmic read Re-Assigner and abundance quantifier☆18Updated last month
- Metagenomics microbial abundance quantification☆27Updated 2 years ago
- ☆16Updated 4 years ago
- Highly sensitive pathogen detection☆12Updated 4 years ago
- SpydrPick: mutual information based detection of pairs of genomic loci co-evolving under a shared selective pressure.☆13Updated 2 years ago
- MUMmer3☆17Updated 3 years ago
- ☆11Updated last month
- Assembly based core genome SNP alignments for bacteria☆25Updated 5 years ago
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆22Updated 2 years ago
- Microbial agile accurate SNP Typer☆29Updated last year
- A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.☆25Updated 2 weeks ago
- Quantifying the significance of genetic variation using probabilistic profile-based methods.☆19Updated 3 years ago
- mSWEEP High-resolution sweep metagenomics using fast probabilistic inference☆14Updated 5 months ago
- SameStr identifies shared strains between pairs of metagenomic samples based on the similarity of SNV profiles.☆17Updated 6 months ago
- metagenome population recombination rate estimation pipeline☆12Updated last week
- Tutorial for bacterial GWAS pipline and bugwas, created for Bodega Bay 2016 NGS workshop☆18Updated 9 years ago
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆26Updated 5 years ago
- RCandy: an R package for visualising homologous recombination events in bacterial genomes☆19Updated 2 years ago
- A mathematically characterized hypothesis test for organism presence/absence in a metagenome☆30Updated last week
- Visualisation application for Klebsiella genotypes generated by Kleborate.☆9Updated 4 years ago
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆23Updated 8 months ago
- Strain Prediction and Analysis with Representative SEquence☆18Updated 3 months ago
- Non-redundant pangenome assemblies from multiple genomes or bins☆13Updated last month
- Strain-level haplotyping for metagenomes with short or long-reads.☆50Updated 8 months ago