Targeted sequencing using next-generation sequencing (NGS) platforms offers enormous potential for plant systematics
by enabling economical acquisition of multilocus data sets that can resolve difficult phylogenetic problems. However,
because discovery of single-copy nuclear (SCN) loci from NGS data requires both bioinformatics skills and access to
high-performance computing resources, the application of NGS data has been limited.
MarkerMiner is an easy-to-use, fully automated, open-access
bioinformatic workflow and application for effective discovery of SCN loci in flowering plants angiosperms
(flowering plants), from user-provided angiosperm transcriptome assemblies (e.g. OneKP transcriptome assemblies.
It can be run locally or via the web, and its tabular and alignment outputs facilitate efficient
downstream assessments of phylogenetic utility, locus selection, intron-exon boundary prediction, and primer
or probe development.
This repository contains the configuration(s) necessary to build a CentOS 6.6 based Docker image which can be
used to run the MarkerMiner v1.0 pipeline.
Please refer to the Docker Manual
for detailed instructions on instantiating a prconfigured MarkerMiner Docker container to run the supporting job submission web
If you use MarkerMiner in your research, please cite the following manuscript:
Chamala, S., García, N., Godden, G. T., Krishnakumar, V., Jordon-Thaden, I. E., De Smet, R., Barbazuk,
W. B., Soltis, D. E., and Soltis, P. S. (2015) MarkerMiner 1.0: A new application for phylogenetic
marker development using angiosperm transcriptomes, Applications in Plant Sciences, 3(4): 1400115.