indexofire / enasra

get fastq raw data from ena

enasra

Enasra is a tool to download WGS PE raw data from ENA.

Usage

Installation

# install requirements
$ mamba install aspera-cli curl aria2c

# download enasra
$ git clone https://github.com/indexofire/enasra.git

Download data

# create list or you can download a list from NCBI
$ echo -e "DRR178303\nERR044749\nERR2668680" > list

# run pipeline to download
$ ./getsra.sh -i list -d output

# download via ftp, use aria2c to download
$ ./getsra -m ftp -i list -d output

# or you want to run it backend
$ nohup ./getsra.sh -i list -d output &

Checksum

# md5sum check
$ cd output
$ md5sum -c md5sum.txt