(Q40781286)

23 September 2017

dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms (English)

1 reference

23 September 2017

1 reference

1 reference

Jonathan B Puritz

1

1 reference

PMCID

4060032

23 September 2017

Christopher M Hollenbeck

series ordinal

2

1 reference

PMCID

4060032

23 September 2017

John R Gold

series ordinal

3

1 reference

23 September 2017

10 June 2014

1 reference

23 September 2017

1 reference

23 September 2017

2

1 reference

23 September 2017

e431

1 reference

From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline

23 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4060032

ezRAD: a simplified method for genomic genotyping in non-model organisms

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4060032

Genome sequencing and population genomics in non-model organisms

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4060032

CD-HIT: accelerated for clustering the next-generation sequencing data

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4060032

Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4060032

Stacks: building and genotyping Loci de novo from short-read sequences

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4060032

RAD in the realm of next-generation sequencing technologies.

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4060032

The variant call format and VCFtools

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4060032

A framework for variation discovery and genotyping using next-generation DNA sequencing data

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4060032

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4060032

Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4060032

BEDTools: a flexible suite of utilities for comparing genomic features

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4060032

Fast and accurate long-read alignment with Burrows-Wheeler transform

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4060032

The Sequence Alignment/Map format and SAMtools

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4060032

Fast and accurate short read alignment with Burrows-Wheeler transform

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4060032

Rapid SNP discovery and genetic mapping using sequenced RAD markers

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4060032

Next-generation DNA sequencing methods

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4060032

Bioinformatics challenges of new sequencing technology

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4060032

Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4060032

The genome of the sea urchin Strongylocentrotus purpuratus

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4060032

Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4060032

Genotyping-by-sequencing in ecological and conservation genomics.

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4060032

Stacks: an analysis tool set for population genomics

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4060032

Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4060032

Discordant distribution of populations and genetic variation in a sea star with high dispersal potential.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4060032

The impact of next-generation sequencing technology on genetics

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4060032

2b-RAD: a simple and flexible method for genome-wide genotyping

19 August 2018

1 reference

Crossref

https://api.crossref.org/works/10.7717%2FPEERJ.431

Pervasive indels and their evolutionary dynamics after the fish-specific genome duplication

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24949246

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.7717/PEERJ.431

1 reference

23 September 2017

1 reference

23 September 2017

1 reference

PMCID

4060032