This repository houses the code to run SURPI+, a rapid computational pipeline for comprehensive identification of pathogens from clinical metagenomic sequence data. Please download SURPI+ software from here.
☆43Nov 20, 2019Updated 6 years ago
Alternatives and similar repositories for SURPI-plus-dist
Users that are interested in SURPI-plus-dist are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- SURPI☆86May 10, 2016Updated 10 years ago
- Clin-mNGS: Automated pipeline for pathogen detection from clinical metagenomic data☆19Jun 29, 2021Updated 5 years ago
- VGEA (Viral Genomes Easily Analyzed) is a pipeline for analysis of RNA virus next-generation sequencing data.☆20Sep 12, 2021Updated 4 years ago
- ☆12Jan 29, 2020Updated 6 years ago
- Nanopore read de-multiplexer☆13Mar 25, 2020Updated 6 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Creates a simple OTU table from Kraken2 report.☆13Oct 15, 2024Updated last year
- Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens☆40Apr 6, 2026Updated 3 months ago
- Splitting and accelerating the Oxford Nanopore basecaller guppy using CPU with the SLURM job scheduler☆16Jul 1, 2024Updated 2 years ago
- The Zika bioinformatics pipeline☆37Mar 29, 2020Updated 6 years ago
- SARs-CoV-2 Primer schemes☆16May 14, 2025Updated last year
- Portable WDL workflows for IDseq production pipelines☆32Jan 19, 2022Updated 4 years ago
- Tools for analyzing and comparing SARS-CoV-2 phylogenies☆10Nov 21, 2020Updated 5 years ago
- Retrieve sequences flanked by an arbitrary number of primers from a nucleotide collection.☆11Jun 11, 2021Updated 5 years ago
- ☆25Feb 2, 2021Updated 5 years ago
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- ViromeScan allows the user to explore and taxonomically characterize the virome from metagenomic reads, efficiently denoising samples fro…☆13Feb 13, 2023Updated 3 years ago
- A reference viral database (RVDB)☆27Nov 30, 2018Updated 7 years ago
- Detection of viruses from RNA-Seq on human samples☆46Mar 18, 2023Updated 3 years ago
- A GPU-accelerated method for ultrarapid pathogen identification from metagenomic sequences.☆30Jun 4, 2024Updated 2 years ago
- ☆24Apr 13, 2026Updated 3 months ago
- Primer schemes for real-time genome epidemiology☆30Jun 14, 2023Updated 3 years ago
- Code for design of diagnostic PCR primers, and metabarcoding markers.☆63Nov 7, 2023Updated 2 years ago
- Metagenomics/viromics pipeline that focuses on automation, user-friendliness and a clear audit trail. Jovian aims to empower classical bi…☆18Sep 1, 2023Updated 2 years ago
- 🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results☆252Jan 18, 2024Updated 2 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- ☆18Jul 27, 2023Updated 2 years ago
- The ARTIC fieldbioinformatics pipeline☆134Updated this week
- BAMixChecker: A fast and efficient tool for sample matching checkup☆16Jun 12, 2022Updated 4 years ago
- Munge GenBank files into FASTA and tab-separated metadata☆15Feb 5, 2026Updated 5 months ago
- Automatically design multiplex PCR primer pairs for diverse templates☆36May 23, 2024Updated 2 years ago
- Removing PCR duplicates for sequencing reads.☆14Sep 8, 2020Updated 5 years ago
- barcode demultiplexing☆22Jun 4, 2019Updated 7 years ago
- ☆21Apr 2, 2025Updated last year
- ARTIC nanopore protocol for nCoV2019 novel coronavirus☆171Mar 22, 2023Updated 3 years ago
- Simple, predictable pricing with DigitalOcean hosting • AdAlways know what you'll pay with monthly caps and flat pricing. Enterprise-grade infrastructure trusted by 600k+ customers.
- Multiplex Primer Design☆12May 3, 2020Updated 6 years ago
- ConsensusCruncher is a tool that suppresses errors in next-generation sequencing data by using unique molecular identifiers (UMIs) to ama…☆21Sep 28, 2022Updated 3 years ago
- FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomi…☆68Jun 4, 2026Updated last month
- Influenza genome analysis Nextflow workflow☆33Sep 15, 2025Updated 10 months ago
- VarSkip multiplex PCR designs for SARS-CoV-2 sequencing☆15Jun 14, 2022Updated 4 years ago
- A method of assessing sequence complexity based on kmer frequencies☆33Apr 9, 2018Updated 8 years ago
- Highly sensitive pathogen detection☆12Oct 5, 2020Updated 5 years ago