Introduction

Abyss is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes. Mainstream NGS genome assembly software divides sequences into k-mers and then obtains assembled sequences based on the de Bruijn Graph algorithm. When the program is running, the k-mer strings are stored in the memory. Therefore, the memory of the computer must be large enough. Abyss is based on the Bloom filter. Its advantage is that it can perform parallel operations and run multiple stitching tasks at the same time. Therefore, Abyss processes more genes than NGS.

For more information, visit the official Abyss website.

Programming language: C

Brief description: a gene sequence assembler.

Open source license: GPL