Assembly and intrahost/low-frequency variant calling for viral samples
☆165May 13, 2026Updated last month
Alternatives and similar repositories for viralrecon
Users that are interested in viralrecon are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Reference-based consensus creation☆61Jun 2, 2026Updated last week
- A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.☆10Updated this week
- Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data☆188Jun 8, 2026Updated last week
- Assembly of Nanopore Sequencing☆17May 21, 2026Updated 3 weeks ago
- Depth-weighted De-Mixing☆133Updated this week
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), wit…☆91Nov 8, 2023Updated 2 years ago
- Spriggan is a pipeline used for assembly of bacterial whole genome sequence data and identification of antibiotic resistance genes.☆16Updated this week
- Simple bacterial assembly and annotation pipeline☆88Updated this week
- ☆24Feb 2, 2026Updated 4 months ago
- The ARTIC fieldbioinformatics pipeline☆133Apr 28, 2026Updated last month
- Prepares a SARS-CoV-2 submission for GISAID, NCBI or ENA. Can read GISAID or NCBI files, or plain fasta+tsv/csv/xls. Finds files in input…☆36May 1, 2022Updated 4 years ago
- SARs-CoV-2 Primer schemes☆16May 14, 2025Updated last year
- Differential gene expression analysis and pathway analysis of RNAseq data☆32Jul 3, 2025Updated 11 months ago
- Bioinformatics Pipeline and Visualization resources☆65Aug 30, 2024Updated last year
- 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.
- UPHL's Reference Free Pipeline☆28May 22, 2026Updated 3 weeks ago
- Assembly and binning of metagenomes☆302Updated this week
- iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.☆135Jun 2, 2026Updated last week
- Ultrafast Sample Placement on Existing Trees☆140Jun 1, 2026Updated 2 weeks ago
- ☆27Aug 2, 2023Updated 2 years ago
- Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement☆259May 26, 2026Updated 2 weeks ago
- ARTIC SARS-CoV-2 workflow and reporting☆51Apr 25, 2025Updated last year
- Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data☆14Jun 5, 2026Updated last week
- Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health con…☆62Jun 8, 2026Updated last week
- End-to-end encrypted cloud storage - Proton Drive • AdSpecial offer: 40% Off Yearly / 80% Off First Month. Protect your most important files, photos, and documents from prying eyes.
- Read contamination removal☆25Jan 24, 2024Updated 2 years ago
- TADA - Targeted Amplicon Diversity Analysis - a DADA2-focused Nextflow workflow for any targeted amplicon region☆22May 9, 2026Updated last month
- Pipeline to fetch metadata and raw FastQ files from public databases☆194May 29, 2026Updated 2 weeks ago
- Viral Annotation DefineR: classification and annotation of viral sequences based on RefSeq annotation☆115Updated this week
- An SRA tool that takes as input local fastq file from a clinical infection sample, identifies and removes any significant human read, and…☆54Jul 24, 2025Updated 10 months ago
- A flexible pipeline for complete analysis of bacterial genomes☆517May 21, 2026Updated 3 weeks ago
- 🔥🐦🔥PHoeNIx: a platform agnostic pipeline for healthcare-associated and antimicrobial resistant pathogens☆105Updated this week
- A Nextflow pipeline for NGS variant calling on SARS-CoV-2. From FASTQ files to normalized and annotated VCF files from GATK, BCFtools, Lo…☆20Jul 11, 2024Updated last year
- A collection of sequencing protocols and bioinformatic resources for SARS-CoV-2 sequencing.☆347Apr 12, 2023Updated 3 years ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- MycoSNP: Whole Genome Sequencing Analysis of Fungal Isolates☆91Mar 10, 2026Updated 3 months ago
- a tool for designing primer panels for multiplex PCR.☆108Feb 5, 2024Updated 2 years ago
- TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomi…☆75Updated this week
- ARTIC nanopore protocol for nCoV2019 novel coronavirus☆171Mar 22, 2023Updated 3 years ago
- Script for parsing SAM/BAM files for coverage statistics☆16Jun 13, 2023Updated 3 years ago
- Dockerfiles and documentation on tools for public health bioinformatics☆225Updated this week
- VarSkip multiplex PCR designs for SARS-CoV-2 sequencing☆14Jun 14, 2022Updated 4 years ago