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Variant calling using NGS and sequence capture data for population and evolutionary genomic inferences in Norway Spruce ( Picea abies )

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/978-3-319-17157-9openalex-snapshot

Advances in the Understanding of Biological Sciences Using Next Generation Sequencing (NGS) Approaches

inferredcites →https://doi.org/10.1007/978-3-319-17157-9_4openalex-snapshot

Variant Calling Using NGS Data in European Aspen (Populus tremula)

inferredcites →https://doi.org/10.1007/s00439-012-1213-zopenalex-snapshot

A beginners guide to SNP calling from high-throughput DNA-sequencing data

inferredcites →https://doi.org/10.1007/s12561-012-9067-4openalex-snapshot

Single Nucleotide Polymorphism (SNP) Detection and Genotype Calling from Massively Parallel Sequencing (MPS) Data

inferredcites →https://doi.org/10.1007/s13353-015-0292-7openalex-snapshot

Review of alignment and SNP calling algorithms for next-generation sequencing data

inferredcites →https://doi.org/10.1016/j.tig.2007.12.007openalex-snapshot

The impact of next-generation sequencing technology on genetics

inferredcites →https://doi.org/10.1016/j.ygeno.2008.07.001openalex-snapshot

Applications of next-generation sequencing technologies in functional genomics

inferredcites →https://doi.org/10.1017/s0016672300014634openalex-snapshot

The hitch-hiking effect of a favourable gene

inferredcites →https://doi.org/10.1038/jhg.2011.43openalex-snapshot

Evaluation of next-generation sequencing software in mapping and assembly

inferredcites →https://doi.org/10.1038/nature09534openalex-snapshot

A map of human genome variation from population-scale sequencing

inferredcites →https://doi.org/10.1038/nature12211openalex-snapshot

The Norway spruce genome sequence and conifer genome evolution

inferredcites →https://doi.org/10.1038/nbt0509-455openalex-snapshot

How to map billions of short reads onto genomes

inferredcites →https://doi.org/10.1038/ng1558openalex-snapshot

Toward genome-wide SNP genotyping

inferredcites →https://doi.org/10.1038/nmeth0610-479aopenalex-snapshot

Erratum: Visualization of image data from cells to organisms

inferredcites →https://doi.org/10.1038/nmeth0610-479bopenalex-snapshot

Erratum: Sense from sequence reads: methods for alignment and assembly

inferredcites →https://doi.org/10.1038/nmeth1156openalex-snapshot

Next-generation sequencing transforms today's biology

inferredcites →https://doi.org/10.1038/nprot.2016.182openalex-snapshot

DNA sequencing technologies: 2006–2016

inferredcites →https://doi.org/10.1038/nrg.2015.28openalex-snapshot

Harnessing the power of RADseq for ecological and evolutionary genomics

inferredcites →https://doi.org/10.1038/nrg.2016.49openalex-snapshot

Coming of age: ten years of next-generation sequencing technologies

inferredcites →https://doi.org/10.1038/nrg.2016.57openalex-snapshot

A comparison of tools for the simulation of genomic next-generation sequencing data

inferredcites →https://doi.org/10.1038/nrg2986openalex-snapshot

Genotype and SNP calling from next-generation sequencing data

inferredcites →https://doi.org/10.1038/nrg3117openalex-snapshot

Repetitive DNA and next-generation sequencing: computational challenges and solutions

inferredcites →https://doi.org/10.1073/pnas.1014330107openalex-snapshot

Transposable element insertions have strongly affected human evolution

inferredcites →https://doi.org/10.1093/bib/bbq015openalex-snapshot

A survey of sequence alignment algorithms for next-generation sequencing

inferredcites →https://doi.org/10.1093/bioinformatics/btn025openalex-snapshot

SOAP: short oligonucleotide alignment program

inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot

Fast and accurate short read alignment with Burrows–Wheeler transform

inferredcites →https://doi.org/10.1093/bioinformatics/btp336openalex-snapshot

SOAP2: an improved ultrafast tool for short read alignment

inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot

The Sequence Alignment/Map format and SAMtools

inferredcites →https://doi.org/10.1093/bioinformatics/btq033openalex-snapshot

BEDTools: a flexible suite of utilities for comparing genomic features

inferredcites →https://doi.org/10.1093/bioinformatics/btq526openalex-snapshot

SeqEM: an adaptive genotype-calling approach for next-generation sequencing studies

inferredcites →https://doi.org/10.1093/bioinformatics/btr330openalex-snapshot

The variant call format and VCFtools

inferredcites →https://doi.org/10.1093/bioinformatics/btr539openalex-snapshot

Pybedtools: a flexible Python library for manipulating genomic datasets and annotations

inferredcites →https://doi.org/10.1093/gbe/evx260openalex-snapshot

LTR Retrotransposons Show Low Levels of Unequal Recombination and High Rates of Intraelement Gene Conversion in Large Plant Genomes

inferredcites →https://doi.org/10.1093/genetics/123.3.585openalex-snapshot

Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

inferredcites →https://doi.org/10.1093/gigascience/giw015openalex-snapshot

Estimating the total number of phosphoproteins and phosphorylation sites in eukaryotic proteomes

inferredcites →https://doi.org/10.1093/gigascience/giw016openalex-snapshot

An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing

inferredcites →https://doi.org/10.1101/291716openalex-snapshot

Design and evaluation of a large sequence-capture probe set and associated SNPs for diploid and haploid samples of Norway spruce ( Picea abies )

inferredcites →https://doi.org/10.1101/gr.078212.108openalex-snapshot

Mapping short DNA sequencing reads and calling variants using mapping quality scores

inferredcites →https://doi.org/10.1101/gr.081422.108openalex-snapshot

Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history

inferredcites →https://doi.org/10.1101/gr.088013.108openalex-snapshot

SNP detection for massively parallel whole-genome resequencing

inferredcites →https://doi.org/10.1101/gr.107524.110openalex-snapshot

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

inferredcites →https://doi.org/10.1101/gr.111120.110openalex-snapshot

Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads

inferredcites →https://doi.org/10.1101/gr.129684.111openalex-snapshot

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

inferredcites →https://doi.org/10.1109/sfcs.2000.892127openalex-snapshot

Opportunistic data structures with applications

inferredcites →https://doi.org/10.1111/1755-0998.12613openalex-snapshot

Paralogs are revealed by proportion of heterozygotes and deviations in read ratios in genotyping‐by‐sequencing data from natural populations

inferredcites →https://doi.org/10.1111/tpj.14429openalex-snapshot

Genome‐wide association study identified novel candidate loci affecting wood formation in Norway spruce

inferredcites →https://doi.org/10.1146/annurev.genom.8.080706.092416openalex-snapshot

Repetitive Sequences in Complex Genomes: Structure and Evolution

inferredcites →https://doi.org/10.1155/2012/251364openalex-snapshot

Comparison of Next-Generation Sequencing Systems

inferredcites →https://doi.org/10.1186/1479-7364-8-14openalex-snapshot

Validation and assessment of variant calling pipelines for next-generation sequencing

inferredcites →https://doi.org/10.1186/1745-6150-6-19openalex-snapshot

The struggle for life of the genome's selfish architects

inferredcites →https://doi.org/10.1186/gb-2009-10-3-212openalex-snapshot

The need for speed

inferredcites →https://doi.org/10.1186/gb-2009-10-3-r25openalex-snapshot

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

inferredcites →https://doi.org/10.1186/gb-2010-11-10-r99openalex-snapshot

Improved variant discovery through local re-alignment of short-read next-generation sequencing data using SRMA

inferredcites →https://doi.org/10.1186/s12859-016-1097-3openalex-snapshot

Evaluating the necessity of PCR duplicate removal from next-generation sequencing data and a comparison of approaches

inferredcites →https://doi.org/10.1371/journal.pcbi.1000386openalex-snapshot

SHRiMP: Accurate Mapping of Short Color-space Reads

inferredcites →https://doi.org/10.1371/journal.pgen.0020064openalex-snapshot

Balancing Selection and Its Effects on Sequences in Nearby Genome Regions

inferredcites →https://doi.org/10.1371/journal.pgen.1003457openalex-snapshot

Reference-Free Population Genomics from Next-Generation Transcriptome Data and the Vertebrate–Invertebrate Gap

inferredcites →https://doi.org/10.1534/g3.117.300078openalex-snapshot

The Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in Pinaceae

inferredcites →https://doi.org/10.1534/g3.118.200840openalex-snapshot

An Ultra-Dense Haploid Genetic Map for Evaluating the Highly Fragmented Genome Assembly of Norway Spruce (Picea abies )

inferredcites →https://doi.org/10.1534/g3.119.400357openalex-snapshot

Utilization of Tissue Ploidy Level Variation in de Novo Transcriptome Assembly of Pinus sylvestris

inferredcites →https://doi.org/10.1534/genetics.106.065102openalex-snapshot

Multilocus Patterns of Nucleotide Diversity, Linkage Disequilibrium and Demographic History of Norway Spruce [Picea abies (L.) Karst]

inferredcites →https://doi.org/10.1534/genetics.112.140749openalex-snapshot

Disentangling the Roles of History and Local Selection in Shaping Clinal Variation of Allele Frequencies and Gene Expression in Norway Spruce (Picea abies)

inferredcites →https://doi.org/10.1534/genetics.113.159715openalex-snapshot

Sequencing and Assembly of the 22-Gb Loblolly Pine Genome

inferredcites →https://doi.org/10.1534/genetics.116.193227openalex-snapshot

Sequence of the Sugar Pine Megagenome

inferredcites →https://doi.org/10.2307/2531471openalex-snapshot

Principles of Population Genetics.

inferredcites →https://doi.org/10.32614/r.manualsopenalex-snapshot

R: A Language and Environment for Statistical Computing

inferredcites →https://doi.org/10.48550/arxiv.1207.3907openalex-snapshot

Haplotype-based variant detection from short-read sequencing

inferredcites →https://doi.org/10.5281/zenodo.1480535openalex-snapshot

Association Mapping Identified Novel Candidate Loci Affecting Wood Formation In Norway Spruce

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1038/s41437-026-00836-7openalex-snapshot

Minimum marker densities for accurate genomic predictions and heritability estimates in three major North American and European spruce species

inferred← citeshttps://doi.org/10.1038/s41467-024-55020-4openalex-snapshot

Genomic signatures of adaptation in native lizards exposed to human-introduced fire ants

inferred← citeshttps://doi.org/10.1093/gbe/evaa005openalex-snapshot

Demography and Natural Selection Have Shaped Genetic Variation in the Widely Distributed Conifer Norway Spruce (Picea abies)

inferred← citeshttps://doi.org/10.1101/2020.06.25.170902openalex-snapshot

Quantifying adaptive evolution and the effects of natural selection across the Norway spruce genome

inferred← citeshttps://doi.org/10.1101/2025.11.28.691168openalex-snapshot

Optimizing marker density for maximizing the accuracy of genomic prediction and heritability estimates in three major North American and European spruce species

inferred← citeshttps://doi.org/10.1111/2041-210x.14183openalex-snapshot

Automation of tree‐ring detection and measurements using deep learning

inferred← citeshttps://doi.org/10.3389/fpls.2022.841693openalex-snapshot

Identification of Genetic Loci for Sugarcane Leaf Angle at Different Developmental Stages by Genome-Wide Association Study

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