Ultra fast and highly accurate amplicon sequencing pipeline. Choose between several highly accurate OTU calling algorithms, choose from general or spezialized databases to annotate these taxonomically and create a phylogeny of OTUs - all in on single command.
Available with self-installer from http://psbweb05.psb.ugent.be/lotus/index.html
Pipeline to process metagenomic data from raw reads to taxonomic and functional abudnance matrices. However, the way is the quest and MATAFILER offers the assembly-dependent (gene catalog) and assembly-independent (direct mapping to appropriate databases) workflow. Both are useful in specific situations, e.g. the highly complex soil metagenome often cannot be properly assembled and gene catalog based methods will struggle.
Available in alpha stage from https://github.com/hildebra/MATAFILER
RTK (rarefaction toolkit) provides fast and scalable rarefaction and diversity estimation for numerical data. It also has an R interface and can be installed via CRAN or visit github for a commandline implementation: