TRON-Bioinformatics / covigator-ngs-pipelineView external linksLinks
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
Sorting:
- Nextflow pipeline for BWA, BWA2 and STAR alignments☆12Jul 22, 2024Updated last year
- Sequence Indexing engine for Large Omics data☆18Updated this week
- Summarise nucleotide counts at a set of positions in a BAM file to search for mixtures☆13Apr 5, 2022Updated 3 years ago
- Plot allele frequencies in VCF files☆11Jun 4, 2019Updated 6 years ago
- ☆11May 10, 2025Updated 9 months ago
- Bioinformatics Pipeline☆12Oct 7, 2022Updated 3 years ago
- CNV calling algorithm for detection of homozygous and hemizygous deletions from whole exome sequencing data☆12Nov 9, 2025Updated 3 months ago
- The genome annotation service provides automated gene annotation based on the RAST system. This deploys both client and service component…☆11Sep 22, 2020Updated 5 years ago
- app to collapse Pango lineages for reporting☆13Dec 9, 2025Updated 2 months ago
- Analysis pipelines for QTL discovery and GWAS signals interpretation☆12Sep 3, 2024Updated last year
- A Nextflow pipeline to align, merge, and organize large PhIP-Seq datasets☆12Feb 7, 2025Updated last year
- ☆12Nov 20, 2023Updated 2 years ago
- Plotly BioVisualization 🎯 Interactive Needle and Manhattan Plots & Alignment Viewer☆11Feb 28, 2020Updated 5 years ago
- ☆15Dec 3, 2025Updated 2 months ago
- ☆11Aug 18, 2024Updated last year
- Machine-learning-based general bacterial promoter prediction tool.☆53Jun 19, 2023Updated 2 years ago
- I often use some of the self-written programs.☆16Nov 13, 2025Updated 3 months ago
- ☆12Nov 6, 2023Updated 2 years ago
- lncHOME (lncRNA Homology Explorer), a computational pipeline that identifies a unique coPARSE-lncRNA class with conserved genomic locatio…☆12Nov 2, 2023Updated 2 years ago
- R package to BLAST peptide sequences against each other and identify the minimal overlap of aligning regions.☆16Aug 26, 2025Updated 5 months ago
- A Snakemake pipeline for Quality Control of Whole Genome Sequencing data☆14Jan 18, 2022Updated 4 years ago
- Documentation for analyzing SARS-Cov2 samples.☆12Jun 4, 2020Updated 5 years ago
- ☆12Dec 7, 2020Updated 5 years ago
- Simple Manipulation Of Trees☆13Aug 16, 2025Updated 6 months ago
- SARS-CoV-2: detecting recombinations in viruses using large data sets with high sequence similarity☆13Aug 14, 2023Updated 2 years ago
- R package to analyze aberrant splicing junctions in tumor samples to identify neoepitopes☆14Nov 25, 2025Updated 2 months ago
- ☆18Nov 7, 2024Updated last year
- Quality control for phylogenetic analyses☆13Jan 19, 2026Updated 3 weeks ago
- ☆16May 7, 2023Updated 2 years ago
- ☆15Dec 29, 2025Updated last month
- a gatk4 pipeline with NA12878 demo dateset ,conda environment used(no GPU)☆15Aug 28, 2019Updated 6 years ago
- SARs-CoV-2 Primer schemes☆16May 14, 2025Updated 9 months ago
- PredictDB Pipeline for GTEx v7 data☆18Nov 9, 2022Updated 3 years ago
- Extensible quality control dashboard built around FASTQ assessment.☆15May 17, 2019Updated 6 years ago
- Shell wrappers for bulk and 10X single cell NGS pipelines, RNAseq, ChIPseq, ATACseq, CUT&RUN/TAG, WGS, etc.☆16Feb 10, 2026Updated last week
- High-performance stochastic modeling of DNA loop extrusion interactions☆18Dec 22, 2025Updated last month
- Assemble and following pipeline used in wisent genome paper.☆17Dec 23, 2016Updated 9 years ago
- Interpretable prioritization of splice variants in diagnostic next-generation sequencing☆18May 9, 2024Updated last year
- The fastest VCF/BCF parser in R https://doi.org/10.1093/bioinformatics/btae049☆19Jan 9, 2026Updated last month