title: MetaCAA: A clustering-aided methodology for efficient assembly of metagenomic datasets.
abstract: A key challenge in analyzing metagenomics data pertains to assembly of sequenced DNA fragments (i.e. reads) originating from various microbes in a given environmental sample. Several existing methodologies can assemble reads originating from a single genome. However, these methodologies cannot be applied for efficient assembly of metagenomic sequence datasets. In this study, we present MetaCAA - a clustering-aided methodology which helps in improving the quality of metagenomic sequence assembly. MetaCAA initially groups sequences constituting a given metagenome into smaller clusters. Subsequently, sequences in each cluster are independently assembled using CAP3, an existing single genome assembly program. Contigs formed in each of the clusters along with the unassembled reads are then subjected to another round of assembly for generating the final set of contigs. Validation using simulated and real-world metagenomic datasets indicates that MetaCAA aids in improving the overall quality of assembly. A software implementation of MetaCAA is available at https://metagenomics.atc.tcs.com/MetaCAA.
authors.affiliation: Bio-Sciences R&D Division, TCS Innovation Labs, Tata Research Development & Design Centre, Tata Consultancy Services Ltd., 54-B Hadapsar Industrial Estate, Pune 411013, Maharashtra, India. Electronic address: rachamalla.reddy@tcs.com.
authors.forename: Rachamalla Maheedhar
authors.initials: RM
authors.lastname: Reddy
authors.affiliation: Bio-Sciences R&D Division, TCS Innovation Labs, Tata Research Development & Design Centre, Tata Consultancy Services Ltd., 54-B Hadapsar Industrial Estate, Pune 411013, Maharashtra, India. Electronic address: monzoor@atc.tcs.com.
authors.forename: Monzoorul Haque
authors.initials: MH
authors.lastname: Mohammed
authors.affiliation: Bio-Sciences R&D Division, TCS Innovation Labs, Tata Research Development & Design Centre, Tata Consultancy Services Ltd., 54-B Hadapsar Industrial Estate, Pune 411013, Maharashtra, India. Electronic address: sharmila.mande@tcs.com.
authors.forename: Sharmila S
authors.initials: SS
authors.lastname: Mande
mesh_terms: D066264:Datasets as Topic; D054892:Metagenome; D056186:Metagenomics / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
keywords: Algorithms; Cluster analysis; Contig mapping; High-throughput nucleotide sequencing; Metagenomics