File Formats

Table 1. Common DNA data File Formats

Name	data type	link
FASTA	Chromosome data (DNA)	FASTA format
FASTQ	Read data from sequencing machines	FASTQ format
SAM/BAM	Output from aligners	Sequence Alignment/Map Format Specification
GTF	Gene annotation	GENCODE
EMBL	Individual genes and DNA	http://www.bioperl.org/wiki/EMBL_sequence_format
VEP	Variant end predictor	VEP formats
VCF	Variant call format	VEP formats

These are mostly (with the exception of BAM) ASCII files.

We aim to support all these file formats. At present only FASTA is supported through the class boost::genetics::fasta.