The SpeciesPrimer pipeline is intended to help researchers finding specific primer pairs for the detection and quantification of bacterial species in complex ecosystems.
☆49Apr 24, 2024Updated 2 years ago
Alternatives and similar repositories for speciesprimer
Users that are interested in speciesprimer are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Finding regions of similarity between plasmids☆17Jul 15, 2026Updated last month
- Pipeline to design taxon-specific primes in defined bacterial communities.☆26Jan 28, 2025Updated last year
- Code for design of diagnostic PCR primers, and metabarcoding markers.☆65Nov 7, 2023Updated 2 years ago
- Hybrid Assembler for Plasmids☆10Jul 28, 2022Updated 4 years ago
- PCR Primer Quality Control☆76Aug 6, 2026Updated 3 weeks ago
- End-to-end encrypted email - Proton Mail • AdSpecial offer: 40% Off Yearly / 80% Off First Month. All Proton services are open source and independently audited for security.
- software to identify primers that can distinguish genomes☆20Jan 23, 2026Updated 7 months ago
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆28Feb 6, 2023Updated 3 years ago
- Informatic Sequence Classification Trees☆15Jan 23, 2026Updated 7 months ago
- tool to determine optimal refrerence genome given a set of fasta files☆15May 18, 2023Updated 3 years ago
- Small utility script to submit genomes to PHASTER for phage detection☆26Oct 21, 2021Updated 4 years ago
- GPrimer: a fast GPU-based pipeline for primerdesign for qPCR experiments☆11May 28, 2025Updated last year
- Benchmarking different ways of doing read (taxonomic) classification, with a focus on removal of contamination and MTB classification☆14Apr 8, 2024Updated 2 years ago
- Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.☆110Jan 22, 2026Updated 7 months ago
- A simple script to run an alignment with nucmer and visualise its results.☆10Apr 17, 2023Updated 3 years ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- A toolkit for prokaryotic comparative genomics☆52Feb 23, 2026Updated 6 months ago
- Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.☆55Mar 23, 2026Updated 5 months ago
- Targeted Detection and Reconstruction of Plasmids☆22May 7, 2024Updated 2 years ago
- Miscellaneous Perl scripts from 20 years in microbial bioinformatics☆18Jul 16, 2024Updated 2 years ago
- Primer design for standard PCR, bisulphite PCR, QPCR and sequencing☆15Nov 23, 2018Updated 7 years ago
- whole genome MLST analysis☆55Jun 17, 2026Updated 2 months ago
- Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).☆28May 7, 2026Updated 3 months ago
- The CGView Comparison Tool (CCT) is a package for visually comparing bacterial, plasmid, chloroplast, and mitochondrial sequences.☆37Apr 13, 2024Updated 2 years ago
- Prokaryotic Pangenome Analysis☆24Dec 3, 2021Updated 4 years ago
- Bare Metal GPUs on DigitalOcean Gradient AI • AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- A tool to design highly specific PCR primers for the validation of genomic alterations including structural variants☆48May 21, 2017Updated 9 years ago
- BACTpipe: An assembly and annotation pipeline for bacterial genomics☆20Aug 13, 2026Updated 2 weeks ago
- Bioinformatics Tools☆92Updated this week
- RabbitTClust: enabling fast clustering analysis of millions bacteria genomes with MinHash sketches☆54Aug 21, 2026Updated last week
- PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identifi…☆44Jul 23, 2021Updated 5 years ago
- Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads☆66Jan 22, 2026Updated 7 months ago
- An accurate and sensitive bacterial plasmid identification tool based on deep machine-learning of shared k-mers and genomic features.☆50Apr 20, 2023Updated 3 years ago
- Long-read metagenomic analysis☆112Oct 10, 2023Updated 2 years ago
- Fast alignment-free pangenome creation and exploration☆28Apr 16, 2020Updated 6 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆16Jun 26, 2018Updated 8 years ago
- A toolbox for pangenome analysis and threshold evaluation.☆101Jul 8, 2022Updated 4 years ago
- ☆14Jun 14, 2026Updated 2 months ago
- NanoCLUST is an analysis pipeline for UMAP-based classification of amplicon-based full-length 16S rRNA nanopore reads☆117Nov 20, 2023Updated 2 years ago
- Overlapped primer design for entire coding sequence of the gene with specificity check☆13Feb 22, 2022Updated 4 years ago
- Bacterial taxonomy construction and evaluation in R☆16Jan 30, 2024Updated 2 years ago
- MethyScan: A tool for methylation specific PCR primer design and evaluation☆16Aug 20, 2021Updated 5 years ago