NCBI Project Data

Downloading NCBI Sequences

To keep the Dengue-GLUE repository lightweight, NCBI GenBank sequences are not included within it. Follow these steps to download the sequences: To download sequences >= 5Kb in length run:

Mode path: /project/dengue
GLUE> module dengueNcbiImporterGenBankLong import

To download sequences < 5Kb in length run:

Mode path: /project/dengue
GLUE> module dengueNcbiImporterGenBankShort import

These commands will download the sequences into sources named ncbi-nuccore (for longer sequences) or ncbi-nuccore-short (for shorter sequences).

Export the sequences as follows:

Mode path: /project/dengue
GLUE> export source ncbi-nuccore

The sequences will be exported as subdirectories in your current working directory.

Move the exported source folder containing the GenBank XML sequences to your preferred location on your hard drive.

Update the 'import source' statments of the relevant build to point to this new location:

i.e. import source /path/to/directory/ncbi-nuccore-short

For the longer sequences update this file.

For the shorter sequences update this file.

---