Reduced representation approach for identification of genome-wide SNPs and their annotation for economically important traits in Indian Tharparkar cattle

Fast gapped-read alignment with Bowtie 2

Ben Langmead, Steven L. Salzberg · Nature Methods · 2012 · 61.1K citations

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The variant call format and VCFtools

Petr Danecek, Adam Auton, Gonçalo R. Abecasis et al. · Bioinformatics · 2011 · 17.8K citations · Full text

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A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

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Life Sciences, Bioinformatics, Genetics +17

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

Heng Li · Bioinformatics · 2011 · 7.4K citations · Full text

Life Sciences, Biostatistics, Genetics +16

Quality control and preprocessing of metagenomic datasets

Robert Schmieder, Robert A. Edwards · Bioinformatics · 2011 · 5.4K citations · Full text

Life Sciences, Bioinformatics, Molecular Biology +10