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 2 years ago
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 4 months ago
- R package to analyze aberrant splicing junctions in tumor samples to identify neoepitopes☆15Jun 10, 2026Updated 2 months ago
- Annotation of mutated peptide sequences with published or novel potential neoantigen descriptors☆34Jan 27, 2026Updated 7 months ago
- Documentation for analyzing SARS-Cov2 samples.☆12Jun 4, 2020Updated 6 years ago
- Plot allele frequencies in VCF files☆11Apr 13, 2026Updated 4 months ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Exploration of Omics data☆24Dec 10, 2020Updated 5 years ago
- Interpretable prioritization of splice variants in diagnostic next-generation sequencing☆19May 9, 2024Updated 2 years ago
- ☆11Aug 18, 2024Updated 2 years ago
- SARs-CoV-2 Primer schemes☆16May 14, 2025Updated last year
- CNV calling algorithm for detection of homozygous and hemizygous deletions from whole exome sequencing data☆12Nov 9, 2025Updated 9 months ago
- an online cancer cell line catalogue integrating HLA type, predicted neo-epitopes, virus and gene expression☆13Feb 26, 2024Updated 2 years ago
- RhyDB – High-performance analytical database for sequence alignment data☆19Updated this week
- Automated processing of Sanger sequencing data, taxonomic profiling, and generation of microbial strain libraries☆19Jan 4, 2026Updated 7 months ago
- EasyFuse is a pipeline for accurate fusion gene detection from RNA-seq data.☆69Aug 19, 2026Updated last week
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- ☆12Nov 20, 2023Updated 2 years ago
- 7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs☆13Oct 15, 2025Updated 10 months ago
- Extensible quality control dashboard built around FASTQ assessment.☆15May 17, 2019Updated 7 years ago
- Assembly and intrahost/low-frequency variant calling for viral samples☆165Aug 21, 2026Updated last week
- app to collapse Pango lineages for reporting☆13Dec 9, 2025Updated 8 months ago
- Metascape for Bioinformaticians (MSBio)☆14Jun 30, 2021Updated 5 years ago
- Machine-learning-based general bacterial promoter prediction tool.☆55Jun 19, 2023Updated 3 years ago
- Utility to alias and dealias pango lineages☆23Dec 18, 2023Updated 2 years ago
- Interactive, web-based BLAST results visualization tool. Accessible at https://kablammo.wasmuthlab.org.☆66Sep 30, 2022Updated 3 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.
- ☆51Mar 11, 2022Updated 4 years ago
- Prioritizing Copy Number Variants (CNV) using Phenotype and Gene Functional Similarity☆18Mar 10, 2022Updated 4 years ago
- High-performance stochastic modeling of DNA loop extrusion interactions☆18Dec 22, 2025Updated 8 months ago
- ☆17Dec 29, 2025Updated 8 months ago
- TADA - Targeted Amplicon Diversity Analysis - a DADA2-focused Nextflow workflow for any targeted amplicon region☆22May 9, 2026Updated 3 months ago
- Repository for the workshop "Best practices on development"☆15Mar 19, 2015Updated 11 years ago
- ☆12Apr 25, 2026Updated 4 months ago
- Simple Manipulation Of Trees☆14Aug 16, 2025Updated last year
- SARS-CoV-2 workflow for nanopore sequence data☆42Aug 13, 2026Updated 2 weeks ago
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- Shell wrappers for bulk and 10X single cell NGS pipelines, RNAseq, ChIPseq, ATACseq, CUT&RUN/TAG, GWAS, etc.☆17Updated this week
- SARS-CoV-2: detecting recombinations in viruses using large data sets with high sequence similarity☆13Aug 14, 2023Updated 3 years ago
- A toolkit for analyzing architectural stripes☆23Dec 1, 2024Updated last year
- Nextflow pipeline for Mutect2 somatic variant calling best practices☆23Jun 14, 2024Updated 2 years ago
- trackc aims to produce beautiful genome tracks that are highly customizable☆19Jun 6, 2026Updated 2 months ago
- Quality control for phylogenetic analyses☆13Aug 17, 2026Updated last week
- ☆11Sep 7, 2023Updated 2 years ago