A Nextflow pipeline for NGS variant calling on SARS-CoV-2. From FASTQ files to normalized and annotated VCF files from GATK, BCFtools, LoFreq and iVar.
☆20Jul 11, 2024Updated last year
Alternatives and similar repositories for covigator-ngs-pipeline
Users that are interested in covigator-ngs-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:
- Nextflow pipeline for BWA, BWA2 and STAR alignments☆12Apr 10, 2026Updated 3 weeks ago
- R package to analyze aberrant splicing junctions in tumor samples to identify neoepitopes☆14Nov 25, 2025Updated 5 months ago
- Annotation of mutated peptide sequences with published or novel potential neoantigen descriptors☆34Jan 27, 2026Updated 3 months ago
- Documentation for analyzing SARS-Cov2 samples.☆12Jun 4, 2020Updated 5 years ago
- Plot allele frequencies in VCF files☆11Apr 13, 2026Updated 2 weeks ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- Interpretable prioritization of splice variants in diagnostic next-generation sequencing☆18May 9, 2024Updated last year
- A python graphing library for plotting multiple sequence alignments. An app build on top that runs everything in your browser.☆27Mar 22, 2026Updated last month
- SARs-CoV-2 Primer schemes☆16May 14, 2025Updated 11 months ago
- CNV calling algorithm for detection of homozygous and hemizygous deletions from whole exome sequencing data☆12Nov 9, 2025Updated 5 months ago
- High-performance analytical database for sequence alignment data☆18Updated this week
- an online cancer cell line catalogue integrating HLA type, predicted neo-epitopes, virus and gene expression☆12Feb 26, 2024Updated 2 years ago
- EasyFuse is a pipeline for accurate fusion gene detection from RNA-seq data.☆67Apr 9, 2026Updated 3 weeks ago
- ☆12Nov 20, 2023Updated 2 years ago
- 7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs☆13Oct 15, 2025Updated 6 months ago
- 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.
- Assembly and intrahost/low-frequency variant calling for viral samples☆160Updated this week
- app to collapse Pango lineages for reporting☆13Dec 9, 2025Updated 4 months ago
- Machine-learning-based general bacterial promoter prediction tool.☆54Jun 19, 2023Updated 2 years ago
- ☆51Mar 11, 2022Updated 4 years ago
- Interactive, web-based BLAST results visualization tool. Accessible at https://kablammo.wasmuthlab.org.☆66Sep 30, 2022Updated 3 years ago
- Extensible quality control dashboard built around FASTQ assessment.☆15May 17, 2019Updated 6 years ago
- ☆11Updated this week
- ☆15Dec 29, 2025Updated 4 months ago
- ☆21Apr 13, 2026Updated 2 weeks 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.
- High-performance stochastic modeling of DNA loop extrusion interactions☆18Dec 22, 2025Updated 4 months ago
- Simple Manipulation Of Trees☆13Aug 16, 2025Updated 8 months ago
- SARS-CoV-2 workflow for nanopore sequence data☆42Apr 15, 2026Updated 2 weeks ago
- SARS-CoV-2: detecting recombinations in viruses using large data sets with high sequence similarity☆13Aug 14, 2023Updated 2 years ago
- Shell wrappers for bulk and 10X single cell NGS pipelines, RNAseq, ChIPseq, ATACseq, CUT&RUN/TAG, GWAS, etc.☆16Mar 24, 2026Updated last month
- A toolkit for analyzing architectural stripes☆20Dec 1, 2024Updated last year
- A Nextflow workflow for HLA typing using HLA-HD☆15Jul 3, 2024Updated last year
- Nextflow pipeline for Mutect2 somatic variant calling best practices☆23Jun 14, 2024Updated last year
- TADA - Targeted Amplicon Diversity Analysis - a DADA2-focused Nextflow workflow for any targeted amplicon region☆22Apr 9, 2026Updated 3 weeks ago
- 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.
- Quality control for phylogenetic analyses☆13Updated this week
- Summarise nucleotide counts at a set of positions in a BAM file to search for mixtures☆13Apr 5, 2022Updated 4 years ago
- Utility to alias and dealias pango lineages☆23Dec 18, 2023Updated 2 years ago
- ☆11Sep 7, 2023Updated 2 years ago
- Analysis pipelines for QTL discovery and GWAS signals interpretation☆12Sep 3, 2024Updated last year
- Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement☆253Updated this week
- ☆27May 22, 2025Updated 11 months ago