AQME: A forensic mitochondrial DNA analysis tool for next-generation sequencing data

2017 ◽  
Vol 31 ◽  
pp. 189-197 ◽  
Author(s):  
Kimberly Sturk-Andreaggi ◽  
Michelle A. Peck ◽  
Cecilie Boysen ◽  
Patrick Dekker ◽  
Timothy P. McMahon ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Next Generation Sequencing ◽  
Dna Analysis ◽  
Next Generation Sequencing Data ◽  
Analysis Tool ◽  
Next Generation ◽  
Sequencing Data ◽  
Mitochondrial Dna Analysis ◽  
Generation Sequencing

scholarly journals Next Generation Sequencing Mitochondrial DNA Analysis in Autism Spectrum Disorder

2017 ◽  
Vol 10 (8) ◽  
pp. 1338-1343 ◽  
Author(s):  
Ashok Patowary ◽  
Ryan Nesbitt ◽  
Marilyn Archer ◽  
Raphael Bernier ◽  
Zoran Brkanac
Keyword(s):  
Autism Spectrum Disorder ◽  
Mitochondrial Dna ◽  
Next Generation Sequencing ◽  
Dna Analysis ◽  
Autism Spectrum ◽  
Spectrum Disorder ◽  
Next Generation ◽  
Mitochondrial Dna Analysis ◽  
Generation Sequencing

scholarly journals Pathogen–Host Analysis Tool (PHAT): an integrative platform to analyze next-generation sequencing data

2018 ◽  
Vol 35 (15) ◽  
pp. 2665-2667 ◽  
Author(s):  
Christopher M Gibb ◽  
Robert Jackson ◽  
Sabah Mohammed ◽  
Jinan Fiaidhi ◽  
Ingeborg Zehbe
Keyword(s):  
Next Generation Sequencing ◽  
Variant Calling ◽  
Next Generation Sequencing Data ◽  
Analysis Tool ◽  
Next Generation ◽  
Sequencing Data ◽  
Reference File ◽  
Feedback Error ◽  
Ngs Data ◽  
Generation Sequencing

Abstract Summary The Pathogen–Host Analysis Tool (PHAT) is an application for processing and analyzing next-generation sequencing (NGS) data as it relates to relationships between pathogens and their hosts. Unlike custom scripts and tedious pipeline programming, PHAT provides an integrative platform encompassing raw and aligned sequence and reference file input, quality control (QC) reporting, alignment and variant calling, linear and circular alignment viewing, and graphical and tabular output. This novel tool aims to be user-friendly for life scientists studying diverse pathogen–host relationships. Availability and implementation The project is available on GitHub (https://github.com/chgibb/PHAT) and includes convenient installers, as well as portable and source versions, for both Windows and Linux (Debian and RedHat). Up-to-date documentation for PHAT, including user guides and development notes, can be found at https://chgibb.github.io/PHATDocs/. We encourage users and developers to provide feedback (error reporting, suggestions and comments).

scholarly journals VarB: a variation browsing and analysis tool for variants derived from next-generation sequencing data

2012 ◽  
Vol 28 (22) ◽  
pp. 2983-2985 ◽  
Author(s):  
M. D. Preston ◽  
M. Manske ◽  
N. Horner ◽  
S. Assefa ◽  
S. Campino ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation Sequencing Data ◽  
Analysis Tool ◽  
Next Generation ◽  
Sequencing Data ◽  
Generation Sequencing

scholarly journals mtDNA-Server: next-generation sequencing data analysis of human mitochondrial DNA in the cloud

2016 ◽  
Vol 44 (W1) ◽  
pp. W64-W69 ◽  
Author(s):  
Hansi Weissensteiner ◽  
Lukas Forer ◽  
Christian Fuchsberger ◽  
Bernd Schöpf ◽  
Anita Kloss-Brandstätter ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Data Analysis ◽  
Next Generation Sequencing ◽  
Next Generation Sequencing Data ◽  
Next Generation ◽  
Sequencing Data ◽  
Human Mitochondrial Dna ◽  
Generation Sequencing ◽  
Sequencing Data Analysis

scholarly journals Pathogen-Host Analysis Tool (PHAT): an Integrative Platform to Analyze Pathogen-Host Relationships in Next-Generation Sequencing Data

2017 ◽  
Author(s):  
Christopher M. Gibb ◽  
Robert Jackson ◽  
Sabah Mohammed ◽  
Jinan Fiaidhi ◽  
Ingeborg Zehbe
Keyword(s):  
Next Generation Sequencing ◽  
Variant Calling ◽  
Next Generation Sequencing Data ◽  
Analysis Tool ◽  
Next Generation ◽  
Sequencing Data ◽  
Link Type ◽  
Reference File ◽  
Host Relationships ◽  
Generation Sequencing

AbstractSummaryThe Pathogen-Host Analysis Tool (PHAT) is an application for processing and analyzing next-generation sequencing (NGS) data as it relates to relationships between pathogen and host organisms. Unlike custom scripts and tedious pipeline programming, PHAT provides an integrative platform encompassing raw and aligned sequence and reference file input, quality control (QC) reporting, alignment and variant calling, linear and circular alignment viewing, and graphical and tabular output. This novel tool aims to be user-friendly for life scientists studying diverse pathogen-host relationships.Availability and ImplementationThe project is publicly available on GitHub (https://github.com/chgibb/PHAT) and includes convenient installers, as well as portable and source versions, for both Windows and Linux (Debian and RedHat). Up-to-date documentation for PHAT, including user guides and development notes, can be found at https://chgibb.github.io/PHATDocs/. We encourage users and developers to provide feedback (error reporting, suggestions, and comments) using GitHub Issues.ContactLead software developer: [email protected]

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