II.
LibraryProcess overview
Reference · livelib-process:bioinformatics--shotgun-metagenomics
shotgun-metagenomics overview
Shotgun Metagenomics Pipeline - Comprehensive analysis of shotgun metagenomic sequencing data for taxonomic and functional profiling of microbial communities with strain-level resolution.
Attributes
displayName
shotgun-metagenomics
description
Shotgun Metagenomics Pipeline - Comprehensive analysis of shotgun metagenomic sequencing
data for taxonomic and functional profiling of microbial communities with strain-level resolution.
libraryPath
library/specializations/domains/science/bioinformatics/shotgun-metagenomics.js
specialization
bioinformatics
references
- - MetaPhlAn4: https://github.com/biobakery/MetaPhlAn - HUMAnN3: https://huttenhower.sph.harvard.edu/humann/ - Kraken2: https://ccb.jhu.edu/software/kraken2/ - MEGAHIT: https://github.com/voutcn/megahit - CARD Database: https://card.mcmaster.ca/
example
const result = await orchestrate('specializations/domains/science/bioinformatics/shotgun-metagenomics', {
projectName: 'Environmental Microbiome Study',
samples: [{ id: 'sample1', r1: '/data/sample1_R1.fq.gz', r2: '/data/sample1_R2.fq.gz' }],
metadata: { environment: ['soil', 'water'] },
hostGenome: 'GRCh38'
});
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.