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HadrienG / 2019_classifiers_benchmark

Benchmarking of metagenomic classifiers

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Roadmap #1

Open HadrienG opened 6 years ago

HadrienG commented 6 years ago

This issue will track progress on the project evolution. See it as a to-do list for the project

[x] Make a roadmap

Software tested

[ ] Agree on a preliminary list of software to test (#2 )

Databases

[x] How many genomes? (#3 )
[x] Which genomes to select? (#3 )
[x] Download genomes
[ ] Build databases for the selected software

Datasets

[x] Agree on the number of datasets to simulate (#4 )
[x] Agree on the abundance levels (#4 )
[x] Simulate dataets

Benchmarking

[ ] Lay down rules to be able to add software to the test list if needed
[ ] Run the selected software on all the datasets
[ ] Convert output in a common format

Analysis

[ ] Which software on average is more sensitive
[ ] Species / genus / ... levels
[ ] False positives?
[ ] Differences in identifying bacteria / viruses / archaea
[ ] Speed / Memory consumption
[ ] Conclusions and eventual recommendations