Fishing for compliments

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Luis Pedro Coelho

Nov 12, 2020, 5:07:56 AM11/12/20
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Hi everyone,

If you happen to use (or otherwise like) NGLess it would be very helpful if you could give me a 1-2 sentence positive review for my administration.

It can be very short (1-2 sentences) and focus on any aspect of the tool, the manuscript, the concept that you want. I do want to cite you including your name and affiliation, though.

It would be very much appreciated.


Luis Pedro Coelho | Fudan University |

mette Joergensen

Nov 19, 2020, 2:30:45 AM11/19/20
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Thanks for a cice tool. It makes NGS pipeline development easy. I have replaced our old microbiome pipeline which took years to implement with a ngless pipeline in less than a month including implementing some external modules. The new pipeline is also much mere userfriendly and easy to maintain..
Mette Jørgensen
PERSIMUNE Health Informatics
CHIP, Copenhagen University Hospital

Nov 19, 2020, 12:11:56 PM11/19/20
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Dear Luis,

A very nice, complete and user-friendly tool for processing of shotgun metagenomic data. Even if something is unclear to a novel user of the pipeline, the developers are quick to respond and help out with whatever issue.

I also actually had a question (I posted it some weeks ago, but not sure if you had seen it). Would it be possible to have an updated IGC database with annotations from eggNOG mapper v2 (as I am also interested in e.g. CAZy, which is not annotated yet in the current IGC version)? It would be really greatly appreciated if that'd be possible!

Quinten Ducarmon
Leiden University Medical Center, Department of Medical Microbiology
Op donderdag 19 november 2020 om 08:30:45 UTC+1 schreef mette Joergensen:

Ulrike Löber

Nov 19, 2020, 12:20:13 PM11/19/20
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Dear Luis,
Ngless serves very well for the purpose of reproducibility. Once setting up a workflow, it is quite convenient to apply this to similar data.

Dr. Ulrike Löber

Host-microbiome factors in cardiovascular disease
AG Forslund 

Max-Delbrück-Centrum für Molekulare Medizin in der Helmholtz-Gemeinschaft

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Dec 11, 2020, 4:51:13 AM12/11/20
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Hi Luis,

I think NGLess is a great tool due to its efficiency, reproducibility and user-friendly. It can be used by researchers with low knowledge in coding thanks to the example scripts proportioned and also users with bigger knowledge in informatics can create new modules and functionalities. If in the future is there any forum for this user-created modules for NGLess all the scientific community could help to develop functions and solve different problems as it happens with Bioconductor, and that is valuable. Also, for human gut microbiome is a really good tool because it uses the IGC database which is a database specific for human gut microbiome.

Iñigo Oyarzun
Vall d'Hebron Institute Research

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