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https://genohub.com/recommended-sequencing-coverage-by-application/Table 1: Coverage and Read Recommendations by Application
Category | Detection or Application | Recommended Coverage (x) or Reads (millions) | References | Whole genome sequencing | | 15x | Bentley et al., 2008 | | Heterozygous SNVs | 33x | Bentley et al., 2008 | | INDELs | 60x | Feng et al., 2014 | | Genotype calls | 35x | Ajay et al., 2011 | | CNV | 1-8x | Xie et al., 2009; Medvedev at al., 2010 | Whole exome sequencing | | 100x (3x local depth) | Clark et al., 2011; Meynert et al., 2013 | | Heterozygous SNVs | 100x (13x local depth) | Clark et al., 2011; Meynert et al., 2013 | | INDELs | not recommended | Feng et al., 2014 | Transcriptome Sequencing | | 10-25M | Liu Y. et al., 2014; ENCODE 2011 RNA-Seq | | Alternative splicing | 50-100M | Liu Y. et al., 2013; ENCODE 2011 RNA-Seq | | Allele specific expression | 50-100M | Liu Y. et al., 2013; ENCODE 2011 RNA-Seq | | De novo assembly | >100M | Liu Y. et al., 2013; ENCODE 2011 RNA-Seq | DNA Target-Based Sequencing | | 10-14M (sharp peaks); 20-40M (broad marks) | Rozowsky et al., 2009; ENCODE 2011 Genome; Landt et al., 2012 | | Hi-C | 100M | Belton, J.M et al., 2012 | | 4C (Circularized Chromosome Confirmation Capture) | 1-5M | van de Weken, H.J.G. et al., 2012 | | 5C (Chromosome Carbon Capture Carbon Copy) | 15-25M | Sanyal A. et al., 2012 | | ChIA-PET (Chromatin Interaction Analysis by Paired-End Tag Sequencing) | 15-20M | Zhang, J. et al., 2012 | | FAIRE-Seq | 25-55M | ENCODE 2011 Genome; Landt et al., 2012 | | DNAse 1-Seq | 25-55M | Landt et al., 2012 | DNA Methylation Sequencing | | >20M | Long, H.K. et al., 2013 | | MeDIP-Seq | 60M | Taiwo, O. et al., 2012 | | RRBS (Reduced Representation Bisulfite Sequencing) | 10X | ENCODE 2011 Genome | | Bisulfite-Seq | 5-15X; 30X | Ziller, M.J et al., 2015; Epigenomics Road Map | RNA-Target-Based Sequencing | | 10-40M | Cho J. et al., 2012; Eom T. et al., 2013; Sugimoto Y. et al., 2012 | | iCLIP | 5-15M | Sugimoto Y. et al., 2012; Rogelj B. et al., 2012 | | PAR-CLIP | 5-15M | Rogelj B. et al., 2012 | | RIP-Seq | 5-20M | Lu Z. et al., 2014 | Small RNA (microRNA) Sequencing | | ~1-2M | Metpally RPR et al., 2013; Campbell et al., 2015 | | Discovery | ~5-8M | Metpally RPR et al., 2013; Campbell et al., 2015 |
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