[maker-devel] new tool for assembly validation

[Fields, Christopher J]

From Keith Bradnam’s blog:

http://www.acgt.me/blog/2015/5/18/goodbye-cegma-hello-busco

chris

On Jun 1, 2015, at 3:15 PM, Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>> wrote:

Thanks Panos,

I’ve heard good things about BUSCO, in fact someone from the CEGMA/SNAP group recommended we try it instead of CEGMA on a project I’m collaborating on.

Cheers,
Carson


On Jun 1, 2015, at 1:55 PM, Panos Ioannidis <panos.ioannidis at gmail.com<mailto:panos.ioannidis at gmail.com>> wrote:

Hello MAKER users,

Our lab has recently developed a new tool for genome/transcriptome assembly validation called BUSCO (for Benchmarking Universal Single-Copy Orthologs) (busco.ezlab.org<https://urldefense.proofpoint.com/v2/url?u=http-3A__busco.ezlab.org_&d=AwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=AKkb8CF-lF01USB-JaE2pC35TfJN0Hooxv99KwJ5Pbk&s=RbVHeUwGcQW1WqgFdfRnYPPekTRaFr49a8g_G0Ibj5c&e=>). It works in a way similar to CEGMA, but with certain key differences.

One of its important features (that actually "pushed" me to write this post), is that it can train Augustus using the BUSCOs models it identifies in the genome.

The manuscript is accepted in Bioinformatics and will soon be published, but you can already download it from the website above and try it.

And please let me know if you have any questions or problems!

Panos
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