Analysis of the Metatranscriptome of Microbial Communities by Comparison of Different Assembly Tools Reveals Improved Functional Annotation by Chandan Badapanda in Juniper Publishers in Anatomy Physiology & Biochemistry International Journal
Assembling metatranscriptomic or met genomic data is a challenging task considering huge amount of short read data generated through Next Generation Sequencing (NGS) platforms. Met genomic assembly involves new computational challenges due to the uneven read coverage of bacterial strains present in the sample, similarity between different species and dissimilarities between closely related strains of the same bacteria. During recent times, a large diversity of specialized software tools is available for met genomic or metatranscriptomic assembly. Nevertheless, choosing the most appropriate assembly methods can be rather challenging. Thus, we have chosen four highly cited met genomic or metatranscriptomic assembly tools i.e. IDBA-UD, MetaSPAdes, MEGAHIT and CLC Genomics Workbench for this study. The validation of the assembly was performed on various parameters such as percentage of reads that were participated in the assembly, length distribution of scaffolds, assembly size and N50 Value. Further, taxonomic assignment was achieved through Kaiju and functional annotation of genes was achieved through Cognizer. Based on the sensitivity of all the four assemblers towards the assembly size, length distribution, percentage of annotated genes obtained through Kaiju and Cognizer, the assembler tool MetaSPAdes outperforms the other assembly tool.
