sra data downloading_helper scripts (NGS)

This repository contains python scripts to fetch the information (i.e nucleotide sequences, fastq reads, SNP information )stored for Solanum Hugassi including the chloroplast genome.

Running .py scripts

Save the available scripts in your pc and use the following command to run it in a linux enviroment.. python solanum_hugassi_nuc.py

For windows users:

Open your python IDLE, copy code and press F5.

install prefetch to convert SRA into fastq

1: Downloading the source

wget https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current/sratoolkit.current-ubuntu64.tar.gz

2: Extract tar file

tar -xvf sratoolkit.current-ubuntu64.tar.gz

cd sratoolkit.3.0.5-ubuntu64/

export PATH=$PATH:$(pwd)/bin

3: Check version of the prefetch

prefetch --version

Run the py script for fetching fastq files (Solanum_Hugassi_SRA_fastq_files.py)

No NGS data is available in NCBI SRA archive for the Solanum_Hugassii