Hi Joshua,

Do you want to compare the entire genome or just the transcriptome/exome/variation between the two assembled genomes? Or maybe explore both, using the combined evidence to strengthen any conclusions?

These publications are a good overview of the tools/methods available in Galaxy:
https://main.g2.bx.psu.edu/u/webb/p/pipeline
https://main.g2.bx.psu.edu/u/webb/p/aye-aye

The UCSC Genome browser team also creates whole genome comparison maps - pairwise and multiple sequence alignments. These are labeled as "Chains/Nets" and "Conservation" tracks in their browser at http://genome.ucsc.edu. Generating this type of track would most likely need to occur outside of Galaxy - the UCSC team are the best ones to explain the most current processing methods: http://genome.ucsc.edu/contacts.html. Once created, these could be imported and used with Galaxy's tools. These publications have examples about how this is done with MAF data:
https://main.g2.bx.psu.edu/u/dan/p/maf
https://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012 (protocol 5)

Hopefully this offers some useful choices,

Jen
Galaxy team

On 4/28/13 4:58 PM, Joshua Burkhart [uoregon.edu] wrote:
The lab I work with would like to compare a few populations' genomes of a species with an unpublished genome assembly. I have sequence data for each population that was created using only single-size insertion sequences, yielding only short paired-end reads. I was able to create a genome assembly for one of the populations and would like to see how it compares to another closely related species (which has a published genome). I used Augustus (http://bioinf.uni-greifswald.de/augustus/) to produce a GFF annotation for my assembly but am not sure how to best go about comparing my assembly to the published assembly of the other species. Can Galaxy help? Are there other tools that may be of use? I tried using ACT (http://www.sanger.ac.uk/resources/software/act/) but it never finished. These genomes are approximately 1Gbp. Any advice would help.

Thanks,

Joshua Burkhart
 



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