Bmc Genomics
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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. ⋯ 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 .