Analyze Evidence Asociated with CG Assembly

[rskr]

With these CG assemblies, is there a way to analyze the evidence associated the variations that they call? I have no experience with CG assemblies, but I am wondering if there is some sort of way to look at what the evidence that went into their assemblies.

[scordes]

Yes, evidence (i.e. reads and mappings that support called variations) are stored in the EVIDENCE folder. You can see examples of what this looks like in the publicly released 69 genome data, described here:

http://www.completegenomics.com/sequence-data/download-data/

The 69 Genome Data Set Tab describes the public genomes wand where you can download the data. The Documentation Tab provides links to Data File Format information and Assembly Software Release Notes.

You can also convert the reads and mappings in the EVIDENCE folder to SAM format using CGA Tools, our open source Mac/Linux package that can be downloaded from sourceforge here: cgatools.sourceforge.net

And to be clear, we also provide the initial reads and mappings across the entire genome. These are stored in the MAP folder. Again you can see examples in the public data at the link listed above.

[marcowanger]

Thanks scordes.

Is the cgatools officially announced in CG website? (if not, please let people know at the download site)

I previously wanted to find CG assembly but didnt find any info to do that from the download site.

Thanks for telling us the cgatools.

Yes, evidence (i.e. reads and mappings that support called variations) are stored in the EVIDENCE folder. You can see examples of what this looks like in the publicly released 69 genome data, described here:

http://www.completegenomics.com/sequence-data/download-data/

The 69 Genome Data Set Tab describes the public genomes wand where you can download the data. The Documentation Tab provides links to Data File Format information and Assembly Software Release Notes.

You can also convert the reads and mappings in the EVIDENCE folder to SAM format using CGA Tools, our open source Mac/Linux package that can be downloaded from sourceforge here: cgatools.sourceforge.net

And to be clear, we also provide the initial reads and mappings across the entire genome. These are stored in the MAP folder. Again you can see examples in the public data at the link listed above.

[scordes]

Yes CGA Tools is announced on the Complete Genomics website here:

http://www.completegenomics.com/sequence-data/cgatools/

You can download the software and documentation for CGA Tools here:
cgatools.sourceforge.net