Hello! I am Bérénice, the author of following slides.
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Bérénice Batut
Backofen lab retreat
April 2017
Starting point
Finding good metagenomics datasets
to extract new CRISPR-subtypes
Good metagenomics datasets?
- Long sequences
- Enough sequences
- Different organisms
Analysis idea
- DDBJ
- NCBI
- EBI Metagenomics
- MG-Rast
- 3 recent studies
- 2 recent assemblers never benchmarked
Idea for benchmarking
Test of assemblers
Ideas to compare the assemblers
- MetaQUAST statistics
- Number of contigs above various lengths
- Assembly span above various lengths
- N50 lengths
- L50 lengths
- Computation statistics
- Computation time
- Used RAM
- Taxonomic diversity estimation
Still to do
- Run all assemblers on the representative datasets
- Compare the assembler statistics
- Select the more generalist assembler
- Run the selected assemblers on every possible dataset
- (Extract the CRISPR subtypes)
Thank You!
Hello! I am Bérénice, the author of following slides.
This slide does not exist in original deck. It is useful if you are not familiar with Reveal.JS, used here.
The easiest way to navigate this slide deck is by hitting [space]on your keyboard.
