Metagenome Assembly

Introduction

In metagenomics, reads as such (typically Illumina 2 x 150 bp) are usually too short for direct functional characterization. Therefore, we offer metagenome assembly tools as a previous step to gene prediction and functional annotation.

OmicsBox provides two assemblers for this purpose:

• metaSPAdes: a de Bruijn graph assembler that produces higher quality assemblies, i.e. higher Nx values, but requires more computational resources and runtime.
• MEGAHIT: an ultra-fast, memory-efficient assembler suited for large and complex metagenomic datasets.

Both tools assemble the reads into contigs saved as a multi FASTA file. Additionally, Quast is used to generate basic statistics to assess the quality of the assembly, and the resulting PDF report is accompanied by an Nx distribution chart.

References

• van der Walt AJ., van Goethem MW., Ramond JB., Makhalanyane TP., Reva O. and Cowan DA. (2017). Assembling metagenomes, one community at a time. BMC genomics, 18(1), 521.
• Vollmers J., Wiegand S. and Kaster AK. (2017). Comparing and Evaluating Metagenome Assembly Tools from a Microbiologist's Perspective - Not Only Size Matters! PloS one, 12(1), e0169662.