paper.md

title	tags	authors	affiliations	date	bibliography
any2fasta: convert various sequence and alignment formats to FASTA	bioinformatics genomics file format conversion	name orcid affiliation Torsten Seemann 0000-0001-6046-610X 1, 2	name index Melbourne Bioinformatics, The University of Melbourne, Parkville, Australia. 1 name index Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne, Parkville, Australia. 2	18 October 2018	paper.bib

Summary

FASTA is a simple and pervasive plain text file format for storing genetic sequence data [@pearson1988fasta]. There exist many other richer formats for storing sequences and associated annotations and meta-data, such as the Genbank and EMBL flat files (http://www.insdc.org/documents/feature-table). These formats often need to be converted to FASTA for use in downstream software that only handles the FASTA format. Common tools for converting for format conversion are EMBOSS seqret [@rice2000emboss] and readseq [@gilbert2003readseq]. Unfortunately, these tools mangle sequence identifiers containing characters such as | and .. Furthermore, they offer no way to fix the behaviour and have not seen any development activity in years. Custom scripts using the Bioperl [@stajich2002bioperl] or Biopython [@cock2009biopython] libraries are available, but these are heavyweight solutions for a relatively simple problem.

Here, I present a new software tool called any2fasta written as a single Perl script with no dependencies. It can read the Genbank, EMBL, GFF, FASTA, FASTQ and GFA sequence formats, as well as the CLUSTAL and STOCKHOLM sequence alignment formats. The input files can be of mixed type, and may be compressed with gzip, bzip2 or zip. any2fasta is fast because it only parses those parts of the input files needed to extract the sequence and its identifier.

Acknowledgements

This work was supported by a National Health and Medical Research Council of Australia Project Grant (ID 1149991).

References