What it does

Takes a FASTA, QUAL, FASTQ or Standard Flowgram Format (SFF) file and produces a new sequence file (of the same format) where the sequence identifiers have been renamed according to the specified columns in your tabular file.

Any original description is preserved (N/A for the SFF file format).

WARNING: If you have any duplicates in the input sequence file, you will still have duplicate sequences in the output.

WARNING: If the tabular file has more than one new name for any old ID, the last one is used.

WARNING: The old and new names in your tabular file should not contain white space. If they do, only the first word is used as the identifier.

References

If you use this Galaxy tool in work leading to a scientific publication please cite the following papers:

Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology. PeerJ 1:e167 http://dx.doi.org/10.7717/peerj.167

This tool uses Biopython to read and write SFF files, so you may also wish to cite the Biopython application note (and Galaxy too of course):

Cock et al (2009). Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3. http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878.

This tool is available to install into other Galaxy Instances via the Galaxy Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/seq_rename