SqueezeMeta is our metagenomic/metatranscriptomic pipeline, filling all the steps of the analysis from assembly to gene prediction, taxonomic and functional annotations, and binning. SqueezeMeta supports multi-metagenomic analysis, in which several samples can be simultaneously analyzed. SqueezeMeta is a widely used tool, used in the analysis of more than 80 published metagenomes.
Download it from github
or read the Frontiers paper here
SqueezeMeta also includes SQMtools,a R library for easy inspection and manipulation of the results. See the paper here
Coming soon, ShinySQM will allow interactive graphical display of the results, making it possible to share results with remote users.