bookmark GRASP / Guided Reference-based Assembly of Short Peptides Identifies the homologs of a given reference protein sequence in a database of short peptide metagenomic sequences. GRASPx is a fast and accurate homology-search program implementing a simultaneous alignment and assembly framework. The program achieves >30X speedup compared to its predecessor GRASP. GRASPx was applied to a human saliva metagenome dataset and shows superior performance for both recall and precision rates. It allows assembly and search of homologous reads with respect to all protein sequences encoded in a bacterial genome against a moderate-sized metagenomic data set (e.g. ~40 million reads and ~100 bp per read) within approximately 12 h using 16 threads.