Recipes¶
Domain-specific workflows that compose operations and primitives into complete analysis pipelines. Each recipe takes raw inputs (genome files, FASTQ reads) and produces Tracks.
Available recipes¶
| Recipe | Module | Input | Output |
|---|---|---|---|
| CRISPR Guide Design | recipes.crispr |
Genome + nuclease preset | Annotated guide Regions |
| Barcode Counting | recipes.barcode_count |
Barcode library + FASTQ | TableTrack of counts |
| Tn-seq Profiling | recipes.tnseq |
FASTQ + reference FASTA | IntervalTrack of insertion counts |
Presets¶
Recipes are configured via YAML presets loaded from recipes/presets/:
from seqchain.recipes import load_preset, list_presets
list_presets() # ['cas12a', 'spcas9']
preset = load_preset("spcas9")
Pages¶
- CRISPR —
design_guides,interpret_guides,configure_mapper,CRISPRPreset - Barcode Count —
BarcodeCount - Tn-seq —
TnSeqPipeline,TnSeqResult - Preset Management —
load_preset,list_presets,load_chromatin_config