Pathogen-Host Analysis Tool (PHAT): an integrative platform to analyze next-generation sequencing data
- PMID: 30561651
- DOI: 10.1093/bioinformatics/bty1003
Pathogen-Host Analysis Tool (PHAT): an integrative platform to analyze next-generation sequencing data
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).
© The Author(s) 2018. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
Similar articles
-
NGS-QCbox and Raspberry for Parallel, Automated and Rapid Quality Control Analysis of Large-Scale Next Generation Sequencing (Illumina) Data.PLoS One. 2015 Oct 13;10(10):e0139868. doi: 10.1371/journal.pone.0139868. eCollection 2015. PLoS One. 2015. PMID: 26460497 Free PMC article.
-
AUSPP: A universal short-read pre-processing package.J Bioinform Comput Biol. 2019 Dec;17(6):1950037. doi: 10.1142/S0219720019500379. J Bioinform Comput Biol. 2019. PMID: 32019418
-
ChronQC: a quality control monitoring system for clinical next generation sequencing.Bioinformatics. 2018 May 15;34(10):1799-1800. doi: 10.1093/bioinformatics/btx843. Bioinformatics. 2018. PMID: 29300845
-
Alview: Portable Software for Viewing Sequence Reads in BAM Formatted Files.Cancer Inform. 2015 Sep 13;14:105-7. doi: 10.4137/CIN.S26470. eCollection 2015. Cancer Inform. 2015. PMID: 26417198 Free PMC article. Review.
-
Visual programming for next-generation sequencing data analytics.BioData Min. 2016 Apr 27;9:16. doi: 10.1186/s13040-016-0095-3. eCollection 2016. BioData Min. 2016. PMID: 27127540 Free PMC article. Review.
Cited by
-
Single-Domain Antibodies Represent Novel Alternatives to Monoclonal Antibodies as Targeting Agents against the Human Papillomavirus 16 E6 Protein.Int J Mol Sci. 2019 Apr 28;20(9):2088. doi: 10.3390/ijms20092088. Int J Mol Sci. 2019. PMID: 31035322 Free PMC article.
-
An epithelial organoid model with Langerhans cells for assessing virus-host interactions.Philos Trans R Soc Lond B Biol Sci. 2019 May 27;374(1773):20180288. doi: 10.1098/rstb.2018.0288. Philos Trans R Soc Lond B Biol Sci. 2019. PMID: 30955491 Free PMC article.
Publication types
MeSH terms
LinkOut - more resources
Full Text Sources
