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JOURNAL

Evolutionary Bioinformatics

Numericware i: Identical by State Matrix Calculator

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Evolutionary Bioinformatics 2017:13 1176934316688663

Software or database review

Published on 10 Mar 2017

DOI: 10.1177/1176934316688663


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Abstract

We introduce software, Numericware i, to compute identical by state (IBS) matrix based on genotypic data. Calculating an IBS matrix with a large dataset requires large computer memory and takes lengthy processing time. Numericware i addresses these challenges with 2 algorithmic methods: multithreading and forward chopping. The multithreading allows computational routines to concurrently run on multiple central processing unit (CPU) processors. The forward chopping addresses memory limitation by dividing a dataset into appropriately sized subsets. Numericware i allows calculation of the IBS matrix for a large genotypic dataset using a laptop or a desktop computer. For comparison with different software, we calculated genetic relationship matrices using Numericware i, SPAGeDi, and TASSEL with the same genotypic dataset. Numericware i calculates IBS coefficients between 0 and 2, whereas SPAGeDi and TASSEL produce different ranges of values including negative values. The Pearson correlation coefficient between the matrices from Numericware i and TASSEL was high at .9972, whereas SPAGeDi showed low correlation with Numericware i (.0505) and TASSEL (.0587). With a high-dimensional dataset of 500 entities by 10 000 000 SNPs, Numericware i spent 382 minutes using 19 CPU threads and 64 GB memory by dividing the dataset into 3 pieces, whereas SPAGeDi and TASSEL failed with the same dataset. Numericware i is freely available for Windows and Linux under CC-BY 4.0 license at https://figshare.com/s/f100f33a8857131eb2db.



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PDF  (538.89 KB PDF FORMAT)

RIS citation   (ENDNOTE, REFERENCE MANAGER, PROCITE, REFWORKS)

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BibTex citation   (BIBDESK, LATEX)





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