MetaCluster-TA: taxonomic annotation for metagenomic data based on assembly-assisted binning

Yi Wang, Henry Chi Ming Leung, Siu Ming Yiu, Francis Yuk Lun Chin

Taxonomic annotation of reads is an important problem in metagenomic analysis. Existing annotation tools, which rely on the approach of aligning each read to the taxonomic structure, are unable to annotate many reads efficiently and accurately as reads (~100 bp) are short and most of them come from unknown genomes. Previous work has suggested assembling the reads to make longer contigs before annotation. More reads/contigs can be annotated as a longer contig (in Kbp) can be aligned to a taxon even if it is from an unknown species as long as it contains a conserved region of that taxon. Unfortunately existing metagenomic assembly tools are not mature enough to produce long enough contigs. Binning tries to group reads/contigs of similar species together. Intuitively, reads in the same group (cluster) should be annotated to the same taxon and these reads altogether should cover a significant portion of the genome alleviating the problem of short contigs if the quality of binning is high. However, no existing work has tried to use binning results to help solve the annotation problem. This work explores this direction.