Identification of Low-Confidence Regions in the Pig Reference Genome (Sscrofa10.2). (Q36325651)

13 August 2017

Identification of Low-Confidence Regions in the Pig Reference Genome (Sscrofa10.2). (English)

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13 August 2017

6

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13 August 2017

Alan L Archibald

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David A Hume

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David Hume

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3

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Amanda Warr

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1

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Amanda Warr

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13 August 2017

Christelle Robert

2

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PMC publication ID

4662242

13 August 2017

Nader Deeb

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5

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13 August 2017

27 November 2015

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13 August 2017

Frontiers in Genetics

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13 August 2017

6

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13 August 2017

338

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Whole-genome sequencing is more powerful than whole-exome sequencing for detecting exome variants

13 August 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4662242

Large-scale whole-genome sequencing of the Icelandic population

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4662242

A deep catalog of autosomal single nucleotide variation in the pig

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4662242

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4662242

Design and development of exome capture sequencing for the domestic pig (Sus scrofa).

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4662242

A comparative analysis of algorithms for somatic SNV detection in cancer.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4662242

Evolutionary dynamics of copy number variation in pig genomes in the context of adaptation and domestication

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4662242

A comprehensive survey of copy number variation in 18 diverse pig populations and identification of candidate copy number variable genes associated with complex traits

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4662242

Analyses of pig genomes provide insight into porcine demography and evolution

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4662242

A genome-wide detection of copy number variations using SNP genotyping arrays in swine

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4662242

A systematic survey of loss-of-function variants in human protein-coding genes

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4662242

VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4662242

Differential expression in RNA-seq: a matter of depth

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4662242

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4662242

Detection and correction of false segmental duplications caused by genome mis-assembly

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4662242

BEDTools: a flexible suite of utilities for comparing genomic features

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4662242

Single nucleotide differences (SNDs) in the dbSNP database may lead to errors in genotyping and haplotyping studies

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4662242

Fast and accurate short read alignment with Burrows-Wheeler transform

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4662242

Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4662242

High-resolution mapping of copy-number alterations with massively parallel sequencing

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4662242

Mapping and quantifying mammalian transcriptomes by RNA-Seq

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4662242

Fine-scale structural variation of the human genome

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4662242

Discrepancies in dbSNP confirmation rates and allele frequency distributions from varying genotyping error rates and patterns

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4662242

The UCSC Table Browser data retrieval tool

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4662242

dbSNP: the NCBI database of genetic variation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4662242

Sensitive and accurate detection of copy number variants using read depth of coverage

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4662242

Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4662242

Assembly errors cause false tandem duplicate regions in the chicken (Gallus gallus) genome sequence

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4662242

De novo detection of copy number variation by co-assembly.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4662242

22 September 2018

Identifiers

DOI

10.3389/FGENE.2015.00338

1 reference

13 August 2017

1 reference

PMC publication ID

4662242

13 August 2017

PubMed publication ID

26640477

1 reference

PMC publication ID

4662242