This page lists some common genomics tools used in bioinformatics analysis pipelines. For a more comprehensive list see the section genomic tools in my other Repo Team Teri --> link
| Name | Functionality | Phase | Notes | Maintainers |
|---|---|---|---|---|
| GATK | comprehensive set of analysis tools | all | example pipelines on Terra.bio | The Broad Institute |
| HAIL | analysis | end | runs on Spark for scalability | The Broad Institute |
| IGV | visualization | all | can embed in Jupyter notebooks | The Broad Institute |
| Variant Transforms | transform and load vcf files into BigQuery | end | can embed in Jupyter notebooks | Google Cloud |
| VariantSpark | variant discovery | end | binary format | CSIRO Bioinformatics |
| GT-Scan | variant analysis | end | none | CSIRO Bioinformatics |
- 📘IGV (Integrative Genomics Viewer) tool - link from The Broad
Learning how to work with VCF (Variant Call Format) files
link- 📘General reference 'How sequencing works' - link
- 📘GATK tools (from The Broad) to convert genomic files - link - from/to common formats (i.e. paired FASTQ to unmapped BAM, etc...)
- 📘How to generate a BAM - link & image below from The Broad
