Obtaining Sequence Data

You can either bring your sequence of interest or download sequences from online resources. One of the most useful online resources is the NCBI SRA. To do so:

  1. Go to the NCBI SRA website: https://www.ncbi.nlm.nih.gov/sra and search for species/project.

  2. After finding the BioProject/sequence you want, copy the SRA ID under the RUN tab.

  3. Install the SRA toolkit on your system (Mac, Ubuntu, etc.):

sudo apt install sra-toolkit

  1. Download the sequence using the SRA ID (example: SRR29754043):

prefetch SRR29754043
fastq-dump --split-files SRR29754043 -O /your/output/folder
cd /your/output/folder

  1. Check the quality of the fastq files using FastQC:

fastqc *fastq -O SRA_fastq