A plain-language tour of the file formats every genomics project produces — and what each one is for.
Every genomics project leaves a trail of files, and knowing what each one holds makes results far easier to interpret. From a single Sanger trace to terabytes of NGS output, a handful of standard formats carry the entire workflow.
From the instrument
Sanger sequencing produces AB1 trace files — the raw chromatogram peaks for a single read. NGS instruments emit FASTQ: sequences plus per-base quality scores, the universal starting point for short- and long-read analysis.
After alignment and calling
Reads aligned to a reference are stored as SAM, or its compressed binary form BAM (and CRAM for tighter storage). Variants — the differences from the reference — are recorded in VCF, while feature coordinates live in BED and GFF/GTF files.
FASTQ in, VCF out: most of the pipeline is just moving cleanly between well-defined formats.
- AB1 — Sanger chromatogram traces
- FASTQ — raw reads with quality scores
- BAM / CRAM — aligned reads, compressed
- VCF — called variants
- BED / GFF / GTF — genomic features and annotations