Life Sciences NGS Analysis Router

Use this skill as the top-level entrypoint for ambiguous or broad sequencing-analysis requests.

Start Here

Inspect the available inputs before asking the user questions. Look for:

• Illumina run-folder files: RunInfo.xml, RunParameters.xml, SampleSheet.csv, Data/Intensities/BaseCalls
• FASTQs: *.fastq, *.fq, *.fastq.gz, *.fq.gz
• BAM/CRAM/VCF: *.bam, *.cram, *.vcf, *.vcf.gz
• count matrices: matrix.mtx, features.tsv, barcodes.tsv, *.h5, *.h5ad, *.rds
• metadata: sample sheets, design files, target BEDs, reference FASTA/GTF, primer files

Read references/intake-schema.json and references/pipeline-registry.json when forming the route.

Intake Rules

Ask the smallest set of missing questions needed to choose a defensible pipeline. Do not ask the full questionnaire if file inspection already answers a field.