grinder

Description

grinder website

Grinder is a versatile open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms. Features: * shotgun or amplicon (e.g. 16S rRNA) read libraries * omics support to generate genomic, transcriptomic, proteomic, metagenomic, metatranscriptomic or metaproteomic datasets * arbitrary read length distribution and number of reads * simulation of PCR and sequencing errors (chimeras, point mutations, homopolymers) * support for paired-end (mate pair) datasets * specific rank-abundance settings or manually given abundance for each genome, gene or protein * creation of datasets with a given richness (alpha diversity) * related datasets can share a variable number of genomes (beta diversity) * modeling of the bias created by varying genome lengths or gene copy number * profile mechanism to store preferred options * available to biologists or power users through multiple interfaces: GUI, CLI and API

Environment Modules

Run module spider grinder to find out what environment modules are available for this application.

Environment Variables

• HPC_GRINDER_DIR - installation directory
• HPC_GRINDER_BIN - executable directory

Categories

biology, genomics