Hello all,
How we can use publicly available (SRA, ENA)WGS data of viral genome for functional characterization of the viral genome. Share your opinion
Hi!,
You can download all the raw data from the NCBI using the sra toolkit to your server. The general code is:
fastq-dump --outdir /here you write your directory/ --split-files /home/[USER]/ncbi/public/sra/SRR925811.sra
After, you can use different tools to work with this data, you can perform BLAST, make FastQC analysis to confirm the quality of the reads, and the most common way is creating your own assembly with the reads to identify specific genes that your are interested on. For this, you can create for example a DeNovo Assembly and use different software like SOAP De Novo, Trinity...
I hope this can help you.
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