title: CS-SCORE: Rapid identification and removal of human genome contaminants from metagenomic datasets.
abstract: Metagenomic sequencing data, obtained from host-associated microbial communities, are usually contaminated with host genome sequence fragments. Prior to performing any downstream analyses, it is necessary to identify and remove such contaminating sequence fragments. The time and memory requirements of available host-contamination detection techniques are enormous. Thus, processing of large metagenomic datasets is a challenging task. This study presents CS-SCORE--a novel algorithm that can rapidly identify host sequences contaminating metagenomic datasets. Validation results indicate that CS-SCORE is 2-6 times faster than the current state-of-the-art methods. Furthermore, the memory footprint of CS-SCORE is in the range of 2-2.5GB, which is significantly lower than other available tools. CS-SCORE achieves this efficiency by incorporating (1) a heuristic pre-filtering mechanism and (2) a directed-mapping approach that utilizes a novel sequence composition metric (cs-score). CS-SCORE is expected to be a handy 'pre-processing' utility for researchers analyzing metagenomic datasets.
  
  
  BACKGROUND
  For academic users, an implementation of CS-SCORE is freely available at: http://metagenomics.atc.tcs.com/cs-score (or) https://metagenomics.atc.tcs.com/preprocessing/cs-score.
authors.affiliation: Bio-Sciences R&D Division, TCS Innovation Labs, Tata Research Development & Design Centre, 54-B, Hadapsar Industrial Estate, Pune 411 013, Maharashtra, India. Electronic address: monzoor@atc.tcs.com.
authors.forename: Mohammed Monzoorul
authors.initials: MM
authors.lastname: Haque
authors.affiliation: Bio-Sciences R&D Division, TCS Innovation Labs, Tata Research Development & Design Centre, 54-B, Hadapsar Industrial Estate, Pune 411 013, Maharashtra, India. Electronic address: tungadri@atc.tcs.com.
authors.forename: Tungadri
authors.initials: T
authors.lastname: Bose
authors.affiliation: Bio-Sciences R&D Division, TCS Innovation Labs, Tata Research Development & Design Centre, 54-B, Hadapsar Industrial Estate, Pune 411 013, Maharashtra, India. Electronic address: anirban@atc.tcs.com.
authors.forename: Anirban
authors.initials: A
authors.lastname: Dutta
authors.affiliation: Bio-Sciences R&D Division, TCS Innovation Labs, Tata Research Development & Design Centre, 54-B, Hadapsar Industrial Estate, Pune 411 013, Maharashtra, India. Electronic address: siva@atc.tcs.com.
authors.forename: Chennareddy Venkata Siva Kumar
authors.initials: CV
authors.lastname: Reddy
authors.affiliation: Bio-Sciences R&D Division, TCS Innovation Labs, Tata Research Development & Design Centre, 54-B, Hadapsar Industrial Estate, Pune 411 013, Maharashtra, India. Electronic address: sharmila@atc.tcs.com.
authors.forename: Sharmila S
authors.initials: SS
authors.lastname: Mande
mesh_terms: D000465:Algorithms; D015894:Genome, Human; D006801:Humans; D056186:Metagenomics / Q000379:methods*
keywords: Cluster analysis; DNA contamination; Metagenomics; Sequence analysis DNA