Sequencing Data Formats
One-Sentence Definition
Sequencing data formats are the standardized file types that carry reads, alignments, variants, and annotations through a bioinformatics pipeline.
Simple Explanation
Each pipeline step speaks a specific file dialect. Knowing which file holds what makes debugging possible.
Detailed Scientific Explanation
| Format | Holds | Typical step |
|---|---|---|
| FASTA | Sequences (no quality) | Assemblies, references, genes |
| FASTQ | Reads + per-base quality (Phred) | Raw output, QC |
| SAM / BAM / CRAM | Alignments to a reference | Mapping, variant calling |
| VCF / BCF | Variants (SNPs, indels) | Variant Calling in Bacteria |
| GFF3 / GTF / GenBank | Annotations (genes, features) | Genome Annotation |
| BED | Genomic intervals | Coverage, regions |
| Newick / Nexus | Trees | Phylogenetic Tree Building |
| PDB / mmCIF | 3D structures | Structural Bioinformatics |
| BIOM / TSV | Count tables | 16S Amplicon Analysis, Metagenomics |
Phred quality: Q20 = 1% error, Q30 = 0.1% error.
Mechanism
Text or compressed binary containers with defined headers; indexing (.bai, .tbi, .fai) enables random access on huge files.
Clinical Importance
- Reports must be traceable to a specific BAM/VCF + reference version for audits
Research Importance
- Interoperability across tools; submission requirements for public archives
Diagnostic Relevance
- Data retention policy for clinical WGS (raw reads vs assemblies)
AMR Relevance
- Gene calls in a report should be traceable back to contigs/coordinates
Related MOCs
Active Recall Questions
- Difference between FASTA and FASTQ?
- What does Q30 mean?
- Which file holds SNPs?