getSeqENA

-- Download sequences from ENA/SRA databases --

Depedencies

• wget (normally found in Linux OS)
• gzip >= v1.6 (normally found in Linux OS)
• Aspera Connect 2 >= v3.6.1 (optional)
• curl (optional)
• SRA toolkit >= v2.8.2 (optional) (for SRA interaction)
• Samtools = v1.3.1 (for fastq conversion when downloading BAM/CRAM files)
• GNU Awk (optional) (normally found in Linux OS) (for SRA interaction)

Input

To interact directly with ENA, a list of IDs to download needs to be passed to getSeqENA. This can be done through the -l option.

Usage

usage: getSeqENA.py [-h] [--version] -l /path/to/list/ENA_IDs.txt
                    [-o /output/directory/] [-j N]
                    [-a /path/to/asperaweb_id_dsa.openssh]
                    [--downloadLibrariesType PAIRED] [--downloadCramBam]
                    [--downloadInstrumentPlatform ILLUMINA]
                    [--maximumSamples N]
                    [--SRA | --SRAopt]

Get fastq files from ENA using ENA IDs

optional arguments:
  -h, --help            show this help message and exit
  --version             Version information

Required options:
  -l /path/to/list/ENA_IDs.txt, --listENAids /path/to/list/ENA_IDs.txt
                        Path to list containing the ENA_IDs to be downloaded
                        (default: None)

Facultative options:
  -o /output/directory/, --outdir /output/directory/
                        Path for output directory (default: .)
  -j N, --threads N     Number of threads for cram/bam to fastq conversion
                        (default: 1)
  -a /path/to/asperaweb_id_dsa.openssh, --asperaKey /path/to/asperaweb_id_dsa.openssh
                        Tells getSeqENA.py to download fastq files from ENA
                        using Aspera Connect. With this option, the path to
                        Private-key file asperaweb_id_dsa.openssh is provided
                        (normaly found in
                        ~/.aspera/connect/etc/asperaweb_id_dsa.openssh).
                        (default: None)
  --downloadLibrariesType PAIRED
                        Tells getSeqENA.py to download files with specific
                        library layout (default: BOTH)
  --downloadCramBam     Tells getSeqENA.py to also download cram/bam files and
                        convert them to fastq files (default: False)
  --downloadInstrumentPlatform ILLUMINA
                        Tells getSeqENA.py to download files with specific
                        library layout (default: ILLUMINA)
  --maximumSamples N    Tells getSeqENA.py to only download files for N
                        samples (default: None)

SRA download options (one of the following):
  --SRA                 Tells getSeqENA.py to download reads in fastq format
                        only from NCBI SRA database (not recommended)
                        (default: False)
  --SRAopt              Tells getSeqENA.py to download reads from NCBI SRA
                        if the download from ENA fails

Outputs

run.*.log getSeqENA running log file.

getSeqENA.report.txt Report for each sample downloaded, retrieved from ENA data warehouse. It contains the following fields:

• #sample
• run_accession
• instrument_platform
• instrument_model
• library_layout
• library_souce
• extra_run_accession
• nominal_length
• read_count
• base_count
• date_download

Contact

Miguel Machado mpmachado@medicina.ulisboa.pt