II.
LibraryProcess overview
Reference · livelib-process:bioinformatics--wgs-analysis-pipeline
specializations/domains/science/bioinformatics/wgs-analysis-pipeline overview
Whole Genome Sequencing Pipeline - End-to-end pipeline for whole genome sequencing analysis including read alignment, variant calling, annotation, and quality control. Implements GATK best practices with support for germline and somatic workflows.
Attributes
displayName
specializations/domains/science/bioinformatics/wgs-analysis-pipeline
description
Whole Genome Sequencing Pipeline - End-to-end pipeline for whole genome sequencing analysis
including read alignment, variant calling, annotation, and quality control. Implements GATK best practices
with support for germline and somatic workflows.
libraryPath
library/specializations/domains/science/bioinformatics/wgs-analysis-pipeline.js
specialization
bioinformatics
references
- - GATK Best Practices: https://gatk.broadinstitute.org/hc/en-us/sections/360007226651-Best-Practices-Workflows
- - BWA-MEM2: https://github.com/bwa-mem2/bwa-mem2
- - DeepVariant: https://github.com/google/deepvariant
- - VEP Documentation: https://www.ensembl.org/info/docs/tools/vep/index.html
- - Genome in a Bottle: https://www.nist.gov/programs-projects/genome-bottle
example
const result = await orchestrate('specializations/domains/science/bioinformatics/wgs-analysis-pipeline', {
projectName: 'Cancer Genomics Study',
sampleIds: ['SAMPLE001', 'SAMPLE002', 'SAMPLE003'],
referenceGenome: 'GRCh38',
analysisType: 'germline', // 'germline', 'somatic', 'trio'
fastqDir: '/data/fastq',
outputDir: '/results/wgs'
});
usesAgents
- general-purpose
Outgoing edges
lib_applies_to_domain1
- domain:bioinformatics·DomainBioinformatics
lib_belongs_to_specialization2
- specialization:biomedical-informatics·SpecializationBiomedical Informatics
- specialization:bioinformatics·SpecializationBioinformatics
lib_implements_workflow1
- workflow:experiment-design·WorkflowExperiment Design
lib_involves_role2
- role:research-engineer·RoleResearch Engineer
- role:biomedical-engineer·RoleBiomedical Engineer
lib_requires_skill_area3
- skill-area:data-analysis·SkillAreaData Analysis
- skill-area:statistical-analysis·SkillAreaStatistical Analysis
- skill-area:python-data-pipelines·SkillAreaPython Data Pipelines
Incoming edges
None.