NDLI: A Galaxy-based bioinformatics pipeline for optimised, streamlined microsatellite development from Illumina next-generation sequencing data

Content Provider	Springer Nature Link
Author	Griffiths, Sarah M. Fox, Graeme Briggs, Peter J. Donaldson, Ian J. Hood, Simon Richardson, Pen Leaver, George W. Truelove, Nathan K. Preziosi, Richard F.
Copyright Year	2016
Abstract	Microsatellites are useful tools for ecologists and conservationist biologists, but are taxa-specific and traditionally expensive and time-consuming to develop. New methods using next-generation sequencing (NGS) have reduced these problems, but the plethora of software available for processing NGS data may cause confusion and difficulty for researchers new to the field of bioinformatics. We developed a bioinformatics pipeline for microsatellite development from Illumina paired-end sequences, which is packaged in the open-source bioinformatics tool Galaxy. This optimises and streamlines the design of a microsatellite panel and provides a user-friendly graphical user interface. The pipeline utilises existing programs along with our own novel program and wrappers to: quality-filter and trim reads (Trimmomatic); generate sequence quality reports (FastQC); identify potentially-amplifiable microsatellite loci (Pal_finder); design primers (Primer3); assemble pairs of reads to enhance marker amplification success rates (PANDAseq); and filter optimal loci (Pal_filter). The complete pipeline is freely available for use via a pre-configured Galaxy instance, accessible at https://palfinder.ls.manchester.ac.uk .
Starting Page	481
Ending Page	486
Page Count	6
File Format	PDF
ISSN	18777252
Journal	Conservation Genetics Resources
Volume Number	8
Issue Number	4
e-ISSN	18777260
Language	English
Publisher	Springer Netherlands
Publisher Date	2016-08-02
Publisher Place	Dordrecht
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Microsatellite isolation Pal_finder PANDAseq Trimmomatic Pal_filter Seq-SSR SSRs Galaxy Next-generation sequencing Illumina Conservation Biology/Ecology Ecology Biodiversity Evolutionary Biology Plant Genetics & Genomics Animal Genetics and Genomics
Content Type	Text
Resource Type	Article
Subject	Genetics Ecology, Evolution, Behavior and Systematics

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
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3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

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