Short Read Archive - NCBI

[aloliveira]

I'm working with Illumina and 454 datasets obtained from the NCBI-SRA. And I have a question:

1) The database contains the sequences of adaptors and require a pre-processing before the assembling process?


Thank you,
André

[cliffbeall]

I think it would depend on the experimental design. If you look at the browser it should explain what is there, and certain regions may be depicted in lower case.

For a data set I recently worked with, I executed the sratoolkit fastq-dump command with the --clip option. That automatically removed the key sequence, a barcode and a PCR primer that were part of the experimental design- this was 454 16S rRNA sequencing.