[Biopython] Public example FASTQ files (for Tutorial examples)?

Peter Cock p.j.a.cock at googlemail.com
Fri Mar 25 03:37:00 EDT 2011


Hi all,

One of the volunteers proof reading the Biopython tutorial
noticed our links to specific example FASTQ files at the NCBI
SRA don't work any more. They have withdrawn them from
the FTP site, although you can still download the files in
the compressed *.sra format and in in theory convert then
to FASTQ locally with the NCBI's toolkit (which is cross
platform).

Another option is to download the FASTQ files via the
NCBI's webinterface. Unless there is an obvious way to
do this with a URL that I missed initially, we have a
complicated situation to describe where the user can
choose all the reads for an experiment or just the filtered
set, and also choose to have them pre-trimmed or not.
Plus for me at least, the HTPP download wasn't as
robust as the FTP one was.

I'm hoping someone could suggest a couple of other
moderately sized FASTQ files which are public, on
FTP or a static HTML server, which we can use in
the tutorial.

So, suggestions?

Thanks!

Peter


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