Bioinformatics pipeline for SARS-CoV-2 sequencing at CZ Biohub
☆25Mar 26, 2022Updated 4 years ago
Alternatives and similar repositories for sc2-illumina-pipeline
Users that are interested in sc2-illumina-pipeline are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- QA/QC pipeline for a MiSeq/HiSeq/Ion Torrent/assembly-only run☆12Dec 2, 2024Updated last year
- Read contamination removal☆25Jan 24, 2024Updated 2 years ago
- Luslab nextflow modules☆14Apr 30, 2021Updated 4 years ago
- Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, es…☆42Aug 5, 2024Updated last year
- Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health con…☆62Updated this week
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- Ampseer examines reads in fastq format and identifies which multiplex PCR primer set was used to generate the SARS-CoV-2 sequencing libra…☆15Feb 27, 2024Updated 2 years ago
- Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.☆32Apr 10, 2026Updated last week
- A simple nextflow pipeline for running kraken2 and bracken in a docker container☆20Oct 8, 2025Updated 6 months ago
- ☆27Aug 2, 2023Updated 2 years ago
- ARTIC nanopore protocol for nCoV2019 novel coronavirus☆170Mar 22, 2023Updated 3 years ago
- A message queue for genomic surveillance☆20Oct 14, 2021Updated 4 years ago
- A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), wit…☆91Nov 8, 2023Updated 2 years ago
- interactive barplot for amplicon sequencing☆13Dec 5, 2024Updated last year
- De novo assembly of nanopore reads using nextflow☆20Aug 5, 2020Updated 5 years ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Nextflow plugin implementation skeleton☆11Sep 1, 2025Updated 7 months ago
- Nextflow implementation of the GATK HaplotypeCaller pipeline☆13Dec 27, 2025Updated 3 months ago
- Static website for the PH4AGE alliance☆13Oct 27, 2023Updated 2 years ago
- Finding prophage regions in bacterial genomes using brute force☆22Jan 20, 2023Updated 3 years ago
- ☆15Apr 2, 2025Updated last year
- BACTpipe: An assembly and annotation pipeline for bacterial genomics☆20Dec 3, 2024Updated last year
- ☆10Feb 28, 2018Updated 8 years ago
- Datasets for https://github.com/nextstrain/nextclade☆45Updated this week
- Nextstrain build for dengue virus☆14Updated this week
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- ☆11Oct 21, 2016Updated 9 years ago
- ☆25Jun 25, 2024Updated last year
- A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.☆10Feb 27, 2026Updated last month
- Pipeline for analyzing rare mutations in metagenome-assembled genomes☆10Apr 4, 2025Updated last year
- Intra-species bacterial contamination detection☆25Updated this week
- Ultrafast sequence typing and gene detection from NGS raw reads☆20Apr 15, 2021Updated 5 years ago
- detect temperate phage (active prophage) in assembled bacterial genome sequences☆14Feb 10, 2022Updated 4 years ago
- Rapid identification of Staphylococcus aureus agr locus type and agr operon variants.☆11Jan 6, 2023Updated 3 years ago
- Nanopore read de-multiplexer☆13Mar 25, 2020Updated 6 years ago
- Wordpress hosting with auto-scaling - Free Trial • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- A flexible Nextflow-based framework for the definition of sequencing data processing pipelines☆44Nov 7, 2019Updated 6 years ago
- ☆10Aug 29, 2012Updated 13 years ago
- Workshop content for http://dib-training.readthedocs.org/en/pub/2016-01-13-adv-beg-shell.html☆13Feb 23, 2018Updated 8 years ago
- Collection of R scripts for SARS-CoV-2 (variant) analyses☆12Mar 2, 2023Updated 3 years ago
- ☆13Aug 20, 2025Updated 7 months ago
- Repository for storing latest model, protobuf, designation hash and alias files for pangolin assignments☆32Mar 17, 2026Updated last month
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Jun 26, 2018Updated 7 years ago