Estimating population diversity with CatchAll

Department of Statistical Science, Cornell University, Ithaca, NY, 14853, USA.
Bioinformatics (Impact Factor: 4.62). 02/2012; DOI: 10.1093/bioinformatics/bts075
Source: PubMed

ABSTRACT Motivation: The massive data produced by next-generation sequencing require advanced statistical tools. We address estimating the total diversity or species richness in a population. To date, only relatively simple methods have been implemented in available software. There is a need for software employing modern, computationally intensive statistical analyses including error, goodness-of-fit and robustness assessments. Results: We present CatchAll, a fast, easy-to-use, platform-independent program that computes maximum likelihood estimates for finite-mixture models, weighted linear regression-based analyses and coverage-based non-parametric methods, along with outlier diagnostics. Given sample 'frequency count' data, CatchAll computes 12 different diversity estimates and applies a model-selection algorithm. CatchAll also derives discounted diversity estimates to adjust for possibly uncertain low-frequency counts. It is accompanied by an Excel-based graphics program.

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Available from: James Arthur Foster, Jul 31, 2015
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    • "Parametric alpha diversity estimates for Bacteria and Archaea were calculated using CatchAll version 3 . 2 ( Bunge et al . , 2012 ) , and eukaryotic nonparametric ( Chao2 ) richness estimates ( Chao , 1987 ) were calcu - lated with the program SPADE ( Chao and Shen , 2010 ) . All calculations were performed on pooled sequences from duplicate samples for bacteria and archaea and separate replicated samples for euka - ryotes . We performed these calculations using f"
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    • "The sequences were grouped into operational taxonomic units (OTUs) based on their distances from each other. The estimation of total diversity was performed using the CatchAll program (Bunge et al., 2012). Taxonomic identification of sequences was performed using the RDP Classifier (Cole et al., 2009). "
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