latentstrainanalysis

downloads

Partitioning and analysis methods for large, complex sequence datasets

Home https://github.com/brian-cleary/LatentStrainAnalysis
Versions 0.0.1
License MIT
Recipe https://github.com/bioconda/bioconda-recipes/tree/master/recipes/latentstrainanalysis

LSA was developed as a pre-assembly tool for partitioning metagenomic reads. It uses a hyperplane hashing function and streaming SVD in order to find covariance relations between k-mers. The code, and the process outline in LSFScripts in particular, have been optimized to scale to massive data sets in fixed memory with a highly distributed computing environment.

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install latentstrainanalysis

and update with:

conda update latentstrainanalysis

docker

A Docker container is available at https://quay.io/repository/biocontainers/latentstrainanalysis.