This is the repository for the paper "Pitfalls of genotyping microbial communities with rapidly growing genome collections". All the figures can be reproduced.
git clone https://github.com/zhaoc1/CELL-SYSTEMS-2022.git
cd CELL-SYSTEMS-2022
unzip Rdata.zip
Then the figures.pdf report can be generated by knitting the figures.Rmd in Rstudio.
We also archived a earlier version of midas2 (iggtools v0.5) here.
The cross mapping experiment design is included in the cross_mapping_experiment, which includes simulating reads, read mapping and metagenotyping, and benchmark the precison and recall.