metaphlan for fungus?

[Stef]

Hi,
As I am going to use shotgun data in my project which will also contain fungal seqs, I wonder whether you are working on including specific markers for fungus in the near future. If not, which program would you recommend for fungus instead?
Thanks,
Stef

[Nicola Segata]

Hi Stef,

 yes, we are working on including fungi and viruses into MetaPhlAn. Not there just yet, but this is definitely one of our priorities.

thanks

Nicola

[Stef]

Great! When do you think you will have a first version?
/Stef

[Nicola Segata]

Hi Stef, a safe estimate should be by the end of the year... thanks for your patience!

Nicola

[Nicola Segata]

Hi Chris,

 yes, we are working on the features you mentioned. Additionally, even for microbes alone we will be using more than twice genomic input data comprising 35% more species. Changes in the database we use as source of genomic information, some taxonomic inconsistencies in the available genomes, and several other features we are currently working on are delaying a bit the release of the new major version, but this is our top priority!

thanks

Nicola

On Friday, January 25, 2013 9:18:08 PM UTC+1, Christopher Carr wrote:

Hi Nicola--
I am using MetaPhlAn with soil and acid mine drainage samples. Would love an update to the sequence specific marker database to include fungi, viruses, bacteria, archaea outside the realm of human metagenomes... some area already there (Acidithiobacillus) but not others (Sulfolobus ends up as 100% unclassified).
Thanks,
Chris

P.S. Great tool. Keep up the good work!

[Stef]

Hi Nicola,
I was just wondering how it is going with the fungal markers? I saw the 1.7.7. release but did not see any information on an updated marker database. Can you give a rough date when the fungal markers may be available?
Thanks you!
Stef

[Nicola Segata]

Hi Stef, sorry for the delay, we are doing our best to transition to version 2.0 of MetaPhlAn which will include fungi.

We actually have postdoctoral positions available to work on MetaPhlAn and as soon as we find someone joining the project we will proceed much faster. So if you or someone else in this group happen to know potential candidates please let me know!

thanks

Nicola  

[Zhuofei Xu]

Hi Nicola,

I'm also very interested in the version 2.0 of MetaPhlAn with the fungal markers. Is that possible to be accessible soon?

Thank you!

Zhuofei

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[Nicola Segata]

Hi Zhuofei,

 yes, we are testing MetaPhlAn 2.0 right know including the fungal markers.

more soon

thanks for your patience

Nicola

[Stephen Nayfach]

Hi Nicola,

Is Metaphlan 2.0 available yet? I just returned from the keystone conference and it sounded like 2.0 was up and running.

Thanks,
Stephen

[Nicola Segata]

Hi Stephen,
 yes, we have a public early alpha version available at https://bitbucket.org/biobakery/metaphlan2
We need to finish testing and validating it, but you are welcome to try it out.

cheers
Nicola

[Christel Chehoud]

Hi Nicola,
Thank you for all of your work! Is there any update on when Metaphlan 2 will be released?

Best,
Christel

[Nicola Segata]

Hi Christel,

  MetaPhlAn 2 is in beta testing and available at:

https://bitbucket.org/biobakery/metaphlan2 

many thanks

Nicola