Tag Archives: download

Batch download from NCBI SRA

It has been some time since I’ve posted anything, and I’m trying to start blogging regularly again. I’ve already described how to do a batch submission of data to the NCBI Sequence Read Archive, but today I was trying to do a batch download of a set of SRA sequence data for a project. Turns out, it can be a bit difficult to setup and use the SRA Toolkit, at least in my opinion, but it is certainly easier than uploading data. Fortunately, I found a nice Biostars thread that solved this issue for me, so I figured I’d reiterate it here for my own reference, and that of others.

You can find the thread by visiting https://www.biostars.org/p/111040/.

The command is a long pipe, as follows:

$ esearch -db sra -query <accession> | efetch --format runinfo | cut -d ',' -f 1 | grep SRR | xargs fastq-dump --split-files --bzip2

I’ll break this all down so it is apparent what this command is doing.

  1. First, esearch, part of the NCBI Entrez Direct utilities, queries the database chosen (here, the SRA) with an accession (in the case of a batch, a Bioproject is most appropriate).
  2. The STDOUT from #1 is directed into efetch, which uses this metadata to format a report in the ‘runinfo’ format, which is a comma-separated table of information about the accession.
  3. The STDOUT from #2 is then subsetted, such it splits columns by commas and takes only the first column, which corresponds to the SRR accession numbers.
  4. The STOUT list of SRR accession (#3), plus the header you don’t want, are then sent through grep so that only SRR accession numbers are passed along.
  5. Finally, xargs is used to take the STDOUT from #4 and run fastq-dump, from the NCBI SRA Toolkit, on it. The --split-files argument splits the paired reads into two files, instead of interleaving them, and the --bzip2 flag allows you to compress the output fastq files (you could use –gzip instead).

It is worth pointing out that by correctly setting up your SRA Toolkit configuation, you’ll notice some intermediate files being written to you /path/to/ncbi/sra directory, where the /path/to usually equals $HOME. The ultimate fastq(.gz/bz2) files are written to the directory you called this command from, or to an output directory you can set using fastq-dump (see documentation). This will take some time to actually run on a larger set of files.

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Automated batch download from Ensembl

Recently, I began work on a project that required downloading the genomes of currently sequenced vertebrates. Most of these genomes are available through Ensembl, an online repository of genomes and a website where you can browse genome annotations. In the past, I’ve only had to download a genome or two and always used an ftp connection through the terminal. Here are the commands you can use to do this:
$ cd /path/to/store/data
$ ftp
$ open ftp.ensembl.org
# Username: anonymous
# Password: <email>
# can then move around hierarchy using cd and ls commands
# to download your target file, once you navigate to it, type:
$ mget <file>
# answer y(es) when the server prompts.

If instead you want to download many files at once, you need to take a different approach using a program called rsync (which should be installed on Linux/OSX). Here are the commands you can adapt for your purpose:
$ cd /path/to/store/data
$ rsync -av rsync://ftp.ensembl.org/ensembl/pub/path/to/folder/targetfile.ext ./
# downloads targetfile.ext to your current directory (which is the \\
# path where you want to store data)
$ rsync -av rsync://ftp.ensembl.org/ensembl/pub/path/to/*/*.ext ./
# downloads all files with a .ext extension in all directories \\
# within the path/to/ directory

The command I used to download the most current releases of all complete Ensembl genomes was:
$ rsync -av rsync://ftp.ensembl.org/ensembl/pub/current_fasta/*/dna/*.dna.toplevel.fa.gz ./
You can modify this command to download all soft-masked assemblies, all cDNA assemblies, and many other file types.

One should also note the root directory structure for the Ensembl Genomes database, which includes Metazoans, Protozoans, etc. For Metazoans, it is ‘ftp.ensemblgenomes.org/all/pub/metazoa/current/’ and this can be modified accordingly for the target genome files the user is seeking.

In all cases, these batch rsync downloads are much better than performing the above ftp steps 30+ times and will work in the background. Download rates will vary based on connection and data type, but I would expect to wait between 5 and 10 minutes per assembly file. Hopefully this helps save you some time as well.