Question: Where can I find a small NGS raw data set?
1
gravatar for liorglic
21 months ago by
liorglic40
liorglic40 wrote:

Hi all,

I am looking for a test data set for some software I'm developing, which would be small and simple, but still biologically meaningful. What I need is raw Illumina-style NGS data - basically Fastq format files (paired end). I thought that a phage genome might be a good choice due to it's small size and simplicity, but I couldn't find such data online. Maybe NGS is a bit of an overkill for phage genomes... Any other ideas?
Just to make things clear, I'm not looking for assembled genomes, but rather for the raw data. Any database, publicly-available data set or publication that you know of?
Thanks!

sequencing phage fastq ngs • 1.3k views
ADD COMMENTlink modified 21 months ago by Medhat7.6k • written 21 months ago by liorglic40
2
gravatar for b.nota
21 months ago by
b.nota3.9k
Netherlands
b.nota3.9k wrote:

http://www.ncbi.nlm.nih.gov/sra/?term=phage

ADD COMMENTlink written 21 months ago by b.nota3.9k
1
gravatar for michael.ante
21 months ago by
michael.ante2.5k
Austria/Vienna
michael.ante2.5k wrote:

Hi,

the Bowtie2 aligner comes with a phage example (including data): see here .

Although it's simulated data, it should serve your purposes first. If you need more simulated reads, try the FluxSimulator.

Cheers,

Michael

ADD COMMENTlink written 21 months ago by michael.ante2.5k
1
gravatar for Medhat
21 months ago by
Medhat7.6k
Poland
Medhat7.6k wrote:

This is just example you can search for more specific

http://www.ebi.ac.uk/ena/data/search?query=phage

http://www.illumina.com/informatics/research/sequencing-data-analysis-management/sequencing-data-library.html

http://www.ncbi.nlm.nih.gov/biosample/?term=phage

http://www.ncbi.nlm.nih.gov/sra/?term=phage


also put in your consideration that you can use reference to create artificial reads that suits your needs

https://sourceforge.net/projects/gemsim/

http://www.niehs.nih.gov/research/resources/software/biostatistics/art/

https://sourceforge.net/projects/biogrinder/

ADD COMMENTlink modified 21 months ago • written 21 months ago by Medhat7.6k
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