Skip to content

rtk2 2.10

Choose a tag to compare

View all tags
@hildebra hildebra released this 24 Jan 09:44
· 20 commits to main since this release
v2.10
b9b63aa
This commit was created on GitHub.com and signed with GitHub’s verified signature.
GPG key ID: B5690EEEBB952194
Verified
Learn about vigilant mode.

First release of rtk2

The main difference between rtk (https://github.com/hildebra/Rarefaction) and rtk2 is the focus of rtk2 on matrix operations required for MATATFILER (https://github.com/hildebra/MATAF3). This is implemented in C++ to 1) reduce memory usage 2) support flexible .gz in/output 3) higher speeds 4) multithreaded computations.
General functions include:

  • calculate gene catalog matrix based on cd-hit/mmseqs gene clusters + .bam mappings
  • rarefaction
  • summing subsets of the matrix
  • subselecting columns/rows
  • calculating higher order matrixes based on functional/taxonomic annotations
  • calculating taxa abundances based on median abundances of a set of marker genes and their abundance
  • detect anticorrelated rows to decluter gene matrices
  • normalize matrices of any size
  • .. and other specialized tasks
Assets 2
Loading