4.3 Article

JWES: a new pipeline for whole genome/exome sequence data processing, management, and gene-variant discovery, annotation, prediction, and genotyping

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Editorial Material Multidisciplinary Sciences

A wealth of discovery built on the Human Genome Project - by the numbers

Alexander J. Gates et al.

Summary: The new analysis examines the impact of the draft genome on genomics since 2001, highlighting its effects on publications, drug approvals, and understanding of diseases.

NATURE (2021)

Article Multidisciplinary Sciences

Genomics pipelines to investigate susceptibility in whole genome and exome sequenced data for variant discovery, annotation, prediction and genotyping

Zeeshan Ahmed et al.

Summary: Genomics has been advancing towards an audacious future, transforming biomedical research and disease study. Whole genome sequencing and exome sequencing are two popular methods to detect clinically significant genetic variations. Despite the availability of various bioinformatics applications, timely interpretation of genetic variants remains a challenge for diagnostic laboratories and clinicians. This study assesses the current solutions for processing NGS data for variant identification, alleles, and haplotypes, focusing on standalone and networked bioinformatics applications.
Review Genetics & Heredity

Visualization tools for human structural variations identified by whole-genome sequencing

Toshiyuki T. Yokoyama et al.

JOURNAL OF HUMAN GENETICS (2020)

Article Multidisciplinary Sciences

Precision medicine integrating whole-genome sequencing, comprehensive metabolomics, and advanced imaging

Ying-Chen Claire Hou et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Review Medicine, General & Internal

Bioinformatics and Computational Tools for Next-Generation Sequencing Analysis in Clinical Genetics

Rute Pereira et al.

JOURNAL OF CLINICAL MEDICINE (2020)

Article Gastroenterology & Hepatology

Alterations in Gut Microbiota of Patients With COVID-19 During Time of Hospitalization

Tao Zuo et al.

GASTROENTEROLOGY (2020)

Article Multidisciplinary Sciences

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Matthew H. Bailey et al.

NATURE COMMUNICATIONS (2020)

Article Virology

Evaluation of NGS-based approaches for SARS-CoV-2 whole genome characterisation

Caroline Charre et al.

Summary: Four Next-Generation Sequencing methods have shown excellent performance in SARS-CoV-2 whole-genome sequencing, demonstrating high concordance and suitability for samples with different viral loads. However, it is important to consider the characteristics and validation requirements of each method.

VIRUS EVOLUTION (2020)

Article Microbiology

Coding-Complete Genome Sequences of Three SARS-CoV-2 Strains from Bangladesh

Shahina Akter et al.

MICROBIOLOGY RESOURCE ANNOUNCEMENTS (2020)

Article Microbiology

Four SARS-CoV-2 Genome Sequences from Late April in Stockholm, Sweden, Reveal a Rare Mutation in the Spike Protein

Tatiany Aparecida Teixeira Soratto et al.

MICROBIOLOGY RESOURCE ANNOUNCEMENTS (2020)

Review Biochemical Research Methods

100 Years of evolving gene-disease complexities and scientific debutants

Saman Zeeshan et al.

BRIEFINGS IN BIOINFORMATICS (2020)

Review Biochemistry & Molecular Biology

Genomic Analysis in the Age of Human Genome Sequencing

Tuuli Lappalainen et al.

Review Biochemistry & Molecular Biology

Overview of Genomic Tools for Circular Visualization in the Next-generation Genomic Sequencing Era

Alisha Parveen et al.

CURRENT GENOMICS (2019)

Article Agriculture, Dairy & Animal Science

The GATK joint genotyping workflow is appropriate for calling variants in RNA-seq experiments

Jean-Simon Brouard et al.

JOURNAL OF ANIMAL SCIENCE AND BIOTECHNOLOGY (2019)

Article Clinical Neurology

Utility and implications of exome sequencing in early-onset Parkinson's disease

Joanne Trinh et al.

MOVEMENT DISORDERS (2019)

Article Multidisciplinary Sciences

Comparative analysis of whole-genome sequencing pipelines to minimize false negative findings

Kyu-Baek Hwang et al.

SCIENTIFIC REPORTS (2019)

Article Biotechnology & Applied Microbiology

ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data

Jianhong Ou et al.

BMC GENOMICS (2018)

Article Multidisciplinary Sciences

DNAp: A Pipeline for DNA-seq Data Analysis

Jason L. Causey et al.

SCIENTIFIC REPORTS (2018)

Article Multidisciplinary Sciences

Clinical cancer genomic profiling by three-platform sequencing of whole genome, whole exome and transcriptome

Michael Rusch et al.

NATURE COMMUNICATIONS (2018)

Review Pathology

Genomics pipelines and data integration: challenges and opportunities in the research setting

Jeremy Davis-Turak et al.

EXPERT REVIEW OF MOLECULAR DIAGNOSTICS (2017)

Review Genetics & Heredity

Opportunities and challenges of whole-genome and -exome sequencing

Britt-Sabina Petersen et al.

BMC GENETICS (2017)

Article Biochemical Research Methods

Trimming of sequence reads alters RNA-Seq gene expression estimates

Claire R. Williams et al.

BMC BIOINFORMATICS (2016)

Article Engineering, Biomedical

Faster single-end alignment generation utilizing multi-thread for BWA

Heeseung Jo et al.

BIO-MEDICAL MATERIALS AND ENGINEERING (2015)

Article Multidisciplinary Sciences

A global reference for human genetic variation

David M. Altshuler et al.

NATURE (2015)

Article Multidisciplinary Sciences

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

Aziz Belkadi et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Article Multidisciplinary Sciences

SeqMule: automated pipeline for analysis of human exome/genome sequencing data

Yunfei Guo et al.

SCIENTIFIC REPORTS (2015)

Article Biochemical Research Methods

Buying in to bioinformatics: an introduction to commercial sequence analysis software

David Roy Smith

BRIEFINGS IN BIOINFORMATICS (2015)

Article Biochemical Research Methods

Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony M. Bolger et al.

BIOINFORMATICS (2014)

Article Multidisciplinary Sciences

STORMSeq: An Open-Source, User-Friendly Pipeline for Processing Personal Genomics Data in the Cloud

Konrad J. Karczewski et al.

PLOS ONE (2014)

Article Biochemical Research Methods

WEP: a high-performance analysis pipeline for whole-exome data

Mattia D'Antonio et al.

BMC BIOINFORMATICS (2013)

Article Genetics & Heredity

Sequencing quality assessment tools to enable data-driven informatics for high throughput genomics

Richard M. Leggett et al.

Frontiers in Genetics (2013)

Article Biotechnology & Applied Microbiology

Atlas2 Cloud: a framework for personal genome analysis in the cloud

Uday S. Evani et al.

BMC GENOMICS (2012)

Article Multidisciplinary Sciences

An integrated map of genetic variation from 1,092 human genomes

David M. Altshuler et al.

NATURE (2012)

Article Biochemical Research Methods

The 1000 Genomes Project: data management and community access

Laura Clarke et al.

NATURE METHODS (2012)

Article Multidisciplinary Sciences

SIMPLEX: Cloud-Enabled Pipeline for the Comprehensive Analysis of Exome Sequencing Data

Maria Fischer et al.

PLOS ONE (2012)

Review Genetics & Heredity

Exome sequencing and the genetics of intellectual disability

S. Topper et al.

CLINICAL GENETICS (2011)

Review Genetics & Heredity

What can exome sequencing do for you?

Jacek Majewski et al.

JOURNAL OF MEDICAL GENETICS (2011)

Review Multidisciplinary Sciences

Initial impact of the sequencing of the human genome

Eric S. Lander

NATURE (2011)

Review Genetics & Heredity

Exome sequencing as a tool for Mendelian disease gene discovery

Michael J. Bamshad et al.

NATURE REVIEWS GENETICS (2011)

Article Biochemistry & Molecular Biology

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

Aaron McKenna et al.

GENOME RESEARCH (2010)

Article Multidisciplinary Sciences

A map of human genome variation from population-scale sequencing

David Altshuler et al.

NATURE (2010)

Article Biochemical Research Methods

The Sequence Alignment/Map format and SAMtools

Heng Li et al.

BIOINFORMATICS (2009)

Article Biochemical Research Methods

Fast and accurate short read alignment with Burrows-Wheeler transform

Heng Li et al.

BIOINFORMATICS (2009)

Article Biochemistry & Molecular Biology

Circos: An information aesthetic for comparative genomics

Martin Krzywinski et al.

GENOME RESEARCH (2009)

Review Genetics & Heredity

The impact of next-generation sequencing technology on genetics

Elaine R. Mardis

TRENDS IN GENETICS (2008)

Article Biotechnology & Applied Microbiology

Accuracy and quality of massively parallel DNA pyrosequencing

Susan M. Huse et al.

GENOME BIOLOGY (2007)

Article Biochemistry & Molecular Biology

Galaxy: A platform for interactive large-scale genome analysis

B Giardine et al.

GENOME RESEARCH (2005)

Review Genetics & Heredity

Mapping and sequencing complex genomes: Let's get physical!

BC Meyers et al.

NATURE REVIEWS GENETICS (2004)

Article Multidisciplinary Sciences

Finishing the euchromatic sequence of the human genome

FS Collins et al.

NATURE (2004)

Article Multidisciplinary Sciences

The International HapMap Project

RA Gibbs et al.

NATURE (2003)

Review Multidisciplinary Sciences

The sequence of the human genome

JC Venter et al.

SCIENCE (2001)

Review Multidisciplinary Sciences

Initial sequencing and analysis of the human genome

ES Lander et al.

NATURE (2001)