mInDel

mInDel identifies insertion-deletion (InDel) polymorphisms from next-generation sequencing (NGS) data without requiring a reference genome, enabling InDel marker discovery for genetics research and marker-assisted breeding.

Key Features:

• De novo assembly: Processes raw NGS reads by assembling them into contigs de novo to enable analysis without a reference genome.
• Sliding window alignment: Applies a sliding window alignment strategy on assembled contigs to detect InDel polymorphisms.
• Reference genome independence: Calls InDels without a reference genome, in contrast to reference-dependent tools such as Samtools, GATK, and Atlas2.
• Marker combination option: Provides the ability to combine multiple discovered InDels into single markers to generate larger polymorphisms suitable for gel-based genotyping platforms.
• Short and long InDel detection: Identifies both short and long InDels from assembled contigs.

Scientific Applications:

• Genetics and genomics research: Enables genome-wide discovery of InDels to assess genetic diversity and polymorphism in organisms lacking a reference genome.
• Marker-assisted breeding: Produces InDel markers, including larger combined markers, for tracking traits in breeding programs and gel-based genotyping assays.

Methodology:

mInDel takes raw NGS reads, assembles them into contigs de novo, and applies a sliding window alignment on the contigs to detect short and long InDels.