title: mInDel: a high-throughput and efficient pipeline for genome-wide InDel marker development.
abstract: BACKGROUND
  Rich in genetic information and cost-effective to genotype, the Insertion-Deletion (InDel) molecular marker system is an important tool for studies in genetics, genomics and for marker-assisted breeding. Advent of next-generation sequencing (NGS) revolutionized the speed and throughput of sequence data generation, and enabled genome-wide identification of insertion and deletion variation. However, current NGS-based InDel mining tools, such as Samtools, GATK and Atlas2, all rely on a reference genome for variant calling which hinders their application on unsequenced organisms and the output of short InDels compromised their use on gel-based genotyping platforms. To address these issues, an enhanced platform is needed to identify longer InDels and develop markers in absence of a reference genome.
  
  
  RESULTS
  Here we present mInDel (multiple InDel), a next-generation variant calling tool specifically designed for InDel marker discovery. By taking in raw sequence reads and assembling them into contigs de novo, this software identifies InDel polymorphisms using a sliding window alignment from assembled contigs, rendering a unique advantage when a reference genome is unavailable. By providing an option of combining multiple discovered InDels as output, mInDel is amiable to gel-based genotyping platforms where markers with large polymorphisms are preferred. We demonstrated the usability and performance of this software through a case study using a set of maize NGS data, and experimentally validated the accuracy of markers generated from mInDel.
  
  
  CONCLUSIONS
  mInDel is a novel and practical tool that enables rapid genome-wide InDel marker discovery. The features of being independent from a reference genome and the flexibility with downstream genotyping platforms will allow a broad range of applications across genetics research and plant breeding. The mInDel pipeline is freely available at www.github.com/lyd0527/mInDel .
authors.affiliation: Institute of Agricultural Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
authors.forename: Yuanda
authors.initials: Y
authors.lastname: Lv
authors.affiliation: Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
authors.forename: Yuhe
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Institute of Agricultural Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China. zhaohan@jaas.ac.cn.
authors.forename: Han
authors.initials: H
authors.lastname: Zhao
mesh_terms: D019295:Computational Biology; D005819:Genetic Markers; D060005:Genotyping Techniques; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D054643:INDEL Mutation; D000069600:Plant Breeding; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software; D003313:Zea mays / Q000235:genetics
chemical_list: D005819:Genetic Markers
keywords: Genome-wide marker discovery; Insertions and deletions (InDels); Marker platform; Marker-assisted breeding; Next-generation sequencing (NGS)