How bdaisley/isolater works
isolateR is an R package for processing Sanger marker sequences into quality-controlled results, taxonomic assignments, and microbial strain libraries. Its documented user workflow begins with ABIF (.ab1) files: isoALL wraps quality control, taxonomy assignment, and library generation; the three stages are also available individually. Taxonomy uses type-strain databases and VSEARCH global alignment, while quality and taxonomic stages can export interactive HTML and CSV results. Optional capabilities include FASTA export and phylogenetic tree generation. The graph follows README-documented workflow links; source excerpts were not provided, so uncertain internal wiring is omitted.
Main entry points: isoTAX_function.R Taxonomy assignment · isoQC_function.R Sequence QC · isoALL.R Batch workflow · isoLIB_function.R Strain library
Components 12
Workflow orchestration
- Batch workflow
R/isoALL.R
Sequence analysis
- Sequence QC
R/isoQC_function.R - Taxonomy assignment
R/isoTAX_function.R - Strain library
R/isoLIB_function.R
Results and visualization
- Phylogenetic trees
R/make_tree.R - FASTA export
R/make_fasta.R - Interactive HTML
R/isoQC_function.R - CSV results
Database and utilities
- Type-strain database
R/get_db.R - VSEARCH
R/get_vsearch.R
Other components
- Researcher
- ABIF inputs
Connections 19
- Researcher → Batch workflow: runs workflow
- Researcher → Sequence QC: runs QC
- Researcher → Taxonomy assignment: runs taxonomy
- Researcher → Strain library: builds library
- ABIF inputs → Sequence QC: provides sequences
- Batch workflow → Sequence QC: runs QC
- Batch workflow → Taxonomy assignment: runs taxonomy
- Batch workflow → Strain library: builds library
- Sequence QC → CSV results: exports results
- Sequence QC → FASTA export: exports sequences
- Sequence QC → Interactive HTML: exports report
- CSV results → Taxonomy assignment: provides sequences
- Taxonomy assignment → Type-strain database: searches against
- Taxonomy assignment → VSEARCH: aligns with
- Taxonomy assignment → CSV results: exports assignments
- Taxonomy assignment → Interactive HTML: exports report
- CSV results → Strain library: provides assignments
- Strain library → CSV results: exports library
- Taxonomy assignment → Phylogenetic trees: supports visualization