State of current users of MATAM

[ppericard]

I was surprised to learn there is a current user base of MATAM larger than we were imagining.
@tazend, you were saying your lab is running thousands of jobs simultaneously. I would be more than interested to know more about how you're using MATAM.
As you probably can see, there was not much development of MATAM lately because we thought no one was using it. If there is a real need, we could imagine re-igniting MATAM developments and even applying for grants to recruit a dedicated developer.
Pierre

[mdsufz]

Hi Pierre,

We are using MATAM to reconstruct rRNA (both SSU and LSU) sequences from a huge number of metagenomic libraries (hence the number of jobs). We are curious though why we are getting a lot of files called (core-sga-XXX). I am assuming these are files produced somehwere during the assembly but not sure how they are relevant. If you could provide some input it would be appreciated.

Best regards,
Joao

[ppericard]

Hi,
These are intermediary files produced by the SGA assembler that we use to perform sub-component assemblies. These files are now inevitable, but we had been thinking of using another assembler to perform the same task. However, this could only be done if we restarted actively developing MATAM, which was outside our plans so far. This is why I'm trying to assess if there is a need for the active development of MATAM.
Best,
Pierre

[mdsufz]

Hi Pierre, In our group we always like to use MATAM for reconstructing rRNA genes from our metagenomic datasets. But if we might have to reconsider it if the tool is not going to be further developed. Currently, I am plan to run MATAM on more than 13 000 libraries ;) Best regards, Joao

On 28/03/23 11:40, Pierre Pericard ***@***.***> wrote: Hi, These are intermediary files produced by the SGA assembler that we use to perform sub-component assemblies. These files are now inevitable, but we had been thinking of using another assembler to perform the same task. However, this could only be done if we restarted actively developing MATAM, which was outside our plans so far. This is why I'm trying to assess if there is a need for the active development of MATAM. Best, Pierre — Reply to this email directly, view it on GitHub(#113 (reply in thread) ), or unsubscribe(https://github.com/notifications/unsubscribe-auth/AMXWJGMTYP6DNWDVZOG5TXDW6KWXBANCNFSM6AAAAAAWGIS3HY ). You are receiving this because you commented.Message ID: ***@***.***>

-- Department of Environmental Microbiology Group of Microbial Data Science Helmholtz Centre for Environmental Research - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone: +49 341 235 - 1374 Email: ***@***.*** WWW: http://www.ufz.de

[ppericard]

This gives us food for thought.
We have several choices in front of us:

• we could go the way I have been considering lately: tag MATAM as deprecated and stop developing it altogether. But now that I know there are massive users like your group, and I don't think it exists a real alternative tool, this might not be the chosen route
• we could also provide essential support for the current version, solving bugs and making it easier to use. This would have limited or no impact on the results compared to the current live version. And it would only necessitate moderate developer involvement.
• if there is a need, backed up by users, and we still think this tool is relevant in the current state of the art, we could also consider fully re-start developing MATAM with a dedicated developer. This would allow the implementation of new features or significant optimizations of the current tool. But this would also mean that results from a potential new version could be different (better?) from the current version. And right now, our group does not have many human resources to dedicate to this project, which would mean applying for grants or funding.

I'm curious to hear your thoughts on this.

[mdsufz]

I also don´t know of any alternative (but we also have stuck to using MATAM so I haven´t done an extensive search). I definitely think improvements would be welcome to make it even easier to use and with added features but of course I am aware that human resources are always an issue ;) As for the updated results this wouldn´t be an issue since I don´t think any updates would be made in time for us to run on our datasets. I honestly think that more users should invest some time in using MATAM when dealing with metagenomic libraries as a complementary analysis on taxonomic profiling but that is my humble opinion. I know that sortmerna is also included and I am going to give it a go in the next coming weeks. Hope my two cents at this time help. Cheers, Joao

On 28/03/23 17:59, Pierre Pericard ***@***.***> wrote: This gives us food for thought. We have several choices in front of us: we could go the way I have been considering lately: tag MATAM as deprecated and stop developing it altogether. But now that I know there are massive users like your group, and I don't think it exists a real alternative tool, this might not be the chosen route we could also provide essential support for the current version, solving bugs and making it easier to use. This would have limited or no impact on the results compared to the current live version. And it would only necessitate moderate developer involvement. if there is a need, backed up by users, and we still think this tool is relevant in the current state of the art, we could also consider fully re-start developing MATAM with a dedicated developer. This would allow the implementation of new features or significant optimizations of the current tool. But this would also mean that results from a potential new version could be different (better?) from the current version. And right now, our group does not have many human resources to dedicate to this project, which would mean applying for grants or funding. I'm curious to hear your thoughts on this. — Reply to this email directly, view it on GitHub(#113 (comment) ), or unsubscribe(https://github.com/notifications/unsubscribe-auth/AMXWJGITK5VI6JL4YFGMKGTW6MDHFANCNFSM6AAAAAAWGIS3HY ). You are receiving this because you commented.Message ID: ***@***.***>

-- Department of Environmental Microbiology Group of Microbial Data Science Helmholtz Centre for Environmental Research - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone: +49 341 235 - 1374 Email: ***@***.*** WWW: http://www.ufz.de