Forum:List Of File Formats Used In Bioinformatics?

Question

[veronicaschroeder78]

I have looked and looked through biostars (and googled crazily) and for some reason I cannot find a complete list with file formats used in bioinformatics. There are some lists like http://bioinf.comav.upv.es/courses/sequence_analysis/sequence_file_formats.html or http://www.molecularevolution.org/resources/fileformats but they are rather incomplete or too narrowed.

I was expecting someone compiled a file format database, but I was very disappointed. Do you know more complete lists?

Thanks

[Pierre Lindenbaum]

A new program = a new format :-)

[BioApps]

That's for a reason. Existing file formats are ridiculous! Come on, 'FASTA'? Is there a bigger mistake than this format? Then they replace it with a 'much better' format: FastQ. So, now they now store (large) BINARY data in plain text file! No wonder there are so many FastQ 'formats'. I don't know why bioinformaticians are so afraid of binary files! With the time wasted to scan a single line of text in a FASTQ file to find its true end (LF, CRLF, etc) a program could process over 100 entries in a binary file.

:)

[Pierre Lindenbaum]

also: http://bioinformatics.roslin.ac.uk/lawslaws/ "The first step in developing a new genetic analysis algorithm is to decide how to make the input data file format different from all pre-existing analysis data file formats.""

Answer 1

[Michael]

Have a look at EDAM ontology. You can browse its format concept here: http://bioportal.bioontology.org/ontologies/47814/?p=terms&conceptid=EDAM_format:1915

EDAM (EMBRACE Data and Methods) is an ontology of common bioinformatics operations, topics, types of data including identifiers, and formats.

Answer 2

[Mitch Skinner]

I often end up working from the UCSC file format description page. I don't think there can be a comprehensive list, because people are coming up with new formats all the time.

Answer 3

[Ashutosh Pandey]

There are many but some of the prominent ones especially used in next generation sequencing analysis: 1) Fastq, Fasta format 2) SAM/BAM format 3) VCF format 4) Wig format 5) BED format 6) GTF/GFF3 format