Plastid: nucleotide-resolution analysis of next-generation sequencing and genomics data

BMC Genomics

Table 1 File formats used in genomics

Data type	Format	Implementation
Feature annotations (e.g. genes, transcripts, exons, origins of replication)	BED, extended BED*	Plastid
	BigBed	Plastid + kentUtils [46]
	GTF2*	Plastid
	GFF3*	Plastid
	PSL*	Plastid
Read alignments	bowtie	Plastid
Read alignments	BAM	Plastid + Pysam [27]
Reduced count data	bedGraph	Plastid
	BigWig	Plastid + kentUtils [46]
	wiggle (fixedStep)	Plastid
	wiggle (variableStep)	Plastid
Sequence	FASTA	via Biopython [20]
Sequence	twobit	via twobitreader [21]

For each category of genomics data, many file formats exist. Plastid includes readers for each format that standardize the representation of data for each type, so that the meaning of each data type is separated from its format on disk. *tabix compression for these formats is supported via Pysam [27]

ISSN: 1471-2164