Introduction

GRASShopPER (GPU overlap GRaph ASSembler using Paired End Reads) is the novel assembly method that follows the approach of overlap–layout–consensus (OLC). In the method, a very efficient GPU  implementation of the exact reads alignment algorithm has been used for calculating the scores and shifts on the arcs of the graph. Two-part fork detection strategy has been introduced, which highly reduces misassembly rate in the resulting contigs. The first part is carried out during the graph traversal. In the second part, a greedy hyper-heuristic identifies undetected forks on the basis of paired-end reads information. The results of computational experiments show high coverage of the tested genome.

Download

GRASShopPER can be downloaded at https://sourceforge.net/projects/grasshopper-assembler/

For the complete list of parameters, please follow Readme.txt file under the download link.

System requirements

GRASShopPER requires a computer with graphics processing units, and possibly the environment to run program in parallel manner. Resources used in the assembly process depend on the size of the input library. For example, a genome of bacteria of length 2Mbp requires 17 GB RAM, while one of the human chromosomes requires 82 GB.

Publication

To reference GRASShopPER, please cite:

A. Swiercz, W. Frohmberg, M. Kierzynka, P. Wojciechowski, P. Zurkowski, J. Badura, A. Laskowski, M. Kasprzak, J. Blazewicz, "GRASShopPER. An algorithm for de novo assembly based on GPU alignments", PLOS ONE 13(8): e0202355. 2018 https://doi.org/10.1371/journal.pone.0202355