Pipeline to design taxon-specific primes in defined bacterial communities.
☆25Jan 28, 2025Updated last year
Alternatives and similar repositories for PUPpy
Users that are interested in PUPpy are comparing it to the libraries listed below
Sorting:
- The SpeciesPrimer pipeline is intended to help researchers finding specific primer pairs for the detection and quantification of bacteria…☆45Apr 24, 2024Updated last year
- ☆21Aug 1, 2025Updated 7 months ago
- MAGinator - Accurate SNV calling and profiling of MAGs☆26May 21, 2025Updated 9 months ago
- Reaction Analysis through Imaging of Chemical Units☆16Dec 5, 2025Updated 2 months ago
- Searching large collections of sequencing data with genome-scale queries☆16Feb 5, 2026Updated 3 weeks ago
- ☆63Dec 16, 2025Updated 2 months ago
- Whole genome focused array SNP typer☆14Feb 2, 2026Updated last month
- Visualize microbial evolution at the SNP level!☆15Aug 12, 2025Updated 6 months ago
- Selective and Recursive local Assembler☆15Jan 31, 2022Updated 4 years ago
- ☆11Mar 5, 2025Updated 11 months ago
- Bifrost graph gene caller.☆98Jan 20, 2026Updated last month
- D3 based visualisation for comparative genomics☆15Oct 6, 2016Updated 9 years ago
- More scalable dereplication for metagenome assembled genomes☆77Dec 17, 2025Updated 2 months ago
- Explaining the genetic causality for complex diseases by deep association kernel learning☆15May 7, 2021Updated 4 years ago
- Inferring bacterial recombination rates from large-scale sequencing datasets.☆41Feb 25, 2023Updated 3 years ago
- Code for design of diagnostic PCR primers, and metabarcoding markers.☆63Nov 7, 2023Updated 2 years ago
- scripts for estimating bacteria replication rates based on population genome copy number variation☆73Dec 28, 2019Updated 6 years ago
- Fast implementation of KofamScan optimized for high-memory systems using PyHMMER☆17Jan 13, 2026Updated last month
- ☆17Jul 27, 2023Updated 2 years ago
- ☆44Jun 11, 2025Updated 8 months ago
- An R package for removing contamination from metabarcoding (e.g., microbiome) datasets post-sequencing☆21Oct 17, 2023Updated 2 years ago
- Bacterial GWAS analysis☆47Feb 17, 2026Updated 2 weeks ago
- Accurate and robust inference of microbial growth dynamics from metagenomic sequencing☆19May 11, 2022Updated 3 years ago
- lsaBGC - suite for pan-BGC-omics analysis☆23Nov 21, 2025Updated 3 months ago
- ☆82Nov 27, 2025Updated 3 months ago
- Quantifying the significance of genetic variation using probabilistic profile-based methods.☆19Apr 21, 2021Updated 4 years ago
- TransAnnot - a fast transcriptome annotation pipeline☆20Jan 22, 2025Updated last year
- Interactive, web tool for exploring pan-genome of bacterial strains☆49Jan 14, 2026Updated last month
- BItsliced Genomic Signature Index - Efficient indexing and search in very large collections of WGS data☆124Aug 24, 2023Updated 2 years ago
- Strain-level Metagenomic Estimation of Growth rate (SMEG) measures growth rates of microbial strains from complex metagenomic dataset☆19May 22, 2020Updated 5 years ago
- software to identify primers that can distinguish genomes☆20Jan 23, 2026Updated last month
- ☆21Dec 21, 2022Updated 3 years ago
- Toolbox for comparative genomics of MAGs☆88Feb 24, 2026Updated last week
- Neptune: Genomic Signature Discovery☆21Nov 20, 2024Updated last year
- Bin Chicken - recovery of low abundance and taxonomically targeted metagenome assembled genomes (MAGs) through strategic coassembly☆71Feb 5, 2026Updated 3 weeks ago
- Recentrifuge: robust comparative analysis and contamination removal for metagenomics☆100Feb 10, 2026Updated 3 weeks ago
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆24Feb 6, 2023Updated 3 years ago
- Plot microbiome time series in parallel☆27Nov 7, 2023Updated 2 years ago
- Tutorials on how to use the microGVL to do common bacterial bioinformatic tasks☆25Jun 11, 2024Updated last year