small test data set for genomic SOLiD paired-end sequencing?

[sdvie]

Dear all,

we are implementing a simple mapping/indel-calling pipeline, and in order to test, if everything is in place, I am searching for a handy, manageable dataset as an example or excerpt of a SOLID paired-end genomic DNA sequencing experiment. In detail, I am referring to .csfasta and .qual files of the reads, and optionally a reference (although this should be relatively easy to obtain elsewhere). No matter from which organism, though. I was wondering whether you know of such a data set, maybe as a part of a mapping tool package?
Any idea will be very much appreciated.

cheers,
Sophia

PS.: I found some data sets on the AB website, but unfortunately no genomic paired-end reads.

[NM_010117]

Looking on the SRA website could be a good place to start. A quick search turns up something like this: http://trace.ncbi.nlm.nih.gov/Traces...&run=SRR012744 (SOLID 2x25bp [ftp of the dataset: ftp://ftp-trace.ncbi.nlm.nih.gov/sra...56/SRR011212/]). It's not exactly a small data set, but it's a real-world (1000genomes) and decently manageable one. Also, it's human so obtaining a reference is cake. Mind you it's in sra format, so maybe it's not quite what you're looking for.

[Chipper]

If mate-pair is ok you could try: http://solidsoftwaretools.com/gf/project/ecoli50x50/
Paired-end (50+35 bases from the same fragment) has only been available for a few months so might be hard to find.

[sdvie]

Looking on the SRA website could be a good place to start. A quick search turns up something like this: http://trace.ncbi.nlm.nih.gov/Traces...&run=SRR012744 (SOLID 2x25bp [ftp of the dataset: ftp://ftp-trace.ncbi.nlm.nih.gov/sra...56/SRR011212/]). It's not exactly a small data set, but it's a real-world (1000genomes) and decently manageable one. Also, it's human so obtaining a reference is cake. Mind you it's in sra format, so maybe it's not quite what you're looking for.

Thank you. As far as I know, the sra format can be "unpacked" to fastq using the utility provided by sra, However, I would have to check whether it can also be unpacked to obtain the original separate colorspace reads and qualities files.

If mate-pair is ok you could try: http://solidsoftwaretools.com/gf/project/ecoli50x50/
Paired-end (50+35 bases from the same fragment) has only been available for a few months so might be hard to find.

yes, I spotted this one, too, and might well give it a try. I was not aware that paired-end SOLiD is so recent. Thanks.

[KevinLam]

Thank you. As far as I know, the sra format can be "unpacked" to fastq using the utility provided by sra, However, I would have to check whether it can also be unpacked to obtain the original separate colorspace reads and qualities files.



yes, I spotted this one, too, and might well give it a try. I was not aware that paired-end SOLiD is so recent. Thanks.

well bioinformatically, i guess the data is the same (just insert size diff)

library prep and sequencing adaptors are the new development.
For SOLiD they have directional RNA-seq first .. and I think Illumina is coming up with it soon..