ENA downloader tool

This tool downloads specific samples from ENA. For this, you can download the summary file from any ENA project or search result, from there, subset your target samples or add samples from other ENA summary file and use it to download all your samples with a simple command.

Steps

Download this repo.

git clone https://github.com/AlejandroAb/ENA-downloader-tool.git

Add the Java CLASSPATH according to your download location:

export CLASSPATH=/your/download/location/FOA/build/classes

Display help mEnu

java foa.ENASync --help

#################################################################
###                     ENA Downloader                        ###
###                            v 1.0                          ###
###                                       @company       NIOZ ###
###                                       @author   A. Abdala ###
#################################################################
This program is created to download sequences from ENA archive.Usage:
        java foa.ENASync [options] -s <sumary_file> -o <output_directory>
Options:
        -s      --summary-file          File with the summary of the files to download. Final format TBD
        -o      --out                   Base directory to download the files
        --directory-per-project         It will download the files in one dedicated directory per project.
        --directory-per-sample          It will download the files in one dedicated directory per sample.
                                        If both "directory-per-XXXXX" flags are present, sample directory is created inside project directory
        --library-layout                Paires, Single.
        --library-source                Metagenome, genome, transcriptome, ...
        --library-selection             Random, PCR.
        --library-strategy              Amplicon.
        --filter-library-layout         Filter(exclude) data to download according to this value.
        --filter-library-source         Filter(exclude) data to download according to this value
        --filter-library-selection      Filter(exclude) data to download according to this value
        --filter-library-strategy       Filter(exclude) data to download according to this value
        --data-type                     Raw, functional annotation, taxonomy counts.
        --description                   Description to be applied to the datasets to be download.
        -v      --verbose               Output details during processing

Summary file example

study_accession	sample_accession	experiment_accession	run_accession	tax_id	scientific_name	fastq_ftp	submitted_ftp	sra_ftp
PRJNA377530	SAMN06480931	SRX2614016	SRR5314314	1670606	fungus metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/SRR531/004/SRR5314314/SRR5314314_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR531/004/SRR5314314/SRR5314314_2.fastq.gz		ftp.sra.ebi.ac.uk/vol1/srr/SRR531/004/SRR5314314
PRJNA377530	SAMN06480930	SRX2614017	SRR5314315	1670606	fungus metagenome	ftp.sra.ebi.ac.uk/vol1/fastq/SRR531/005/SRR5314315/SRR5314315_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR531/005/SRR5314315/SRR5314315_2.fastq.gz		ftp.sra.ebi.ac.uk/vol1/srr/SRR531/005/SRR5314315

Download fastq files into rawdata directory

java foa.ENASync -s PEMA_samples.tsv -o rawdata/