Importing Data

Importing data from SRA, ENA or GenBank

If you have download a data set from GenBank, SRA or ENA the format of the sequences headers are different from the raw Roche 454 and Illumina header format. As such, they may or may not be compatible with pRESTO, depending on how the headers have been modified by the sequence archive. The ConvertHeaders allow you to change incompatible header formats into the pRESTO format. For example, to convert from SRA or ENA headers the sra subcommand would be used:

ConvertHeaders.py sra -s reads.fastq

ConvertHeaders provides the following conversion subcommands:

Subcommand	Formats Converted
generic	Headers with an unknown annotation system
454	Roche 454
genbank	NCBI GenBank and RefSeq
illumina	Illumina HiSeq or MiSeq
imgt	IMGT/GENE-DB
sra	NCBI SRA or EMBL-EBI ENA