RFGR: Repeat Finder for Complete and Assembled Whole Genomes and NGS Reads

Area of Science:

• Genomics
• Bioinformatics

Background:

• Repetitive DNA sequences are crucial for genomic instability and serve as genetic markers.
• Identifying these repeats is vital for genome annotation but poses challenges for Next-Generation Sequencing (NGS) data assembly and alignment.

Purpose of the Study:

• To introduce RFGR, a comprehensive tool for detecting exact repetitive DNA sequences in prokaryotic complete genomes, assembled genomes, and NGS reads.
• To demonstrate RFGR's utility in improving genome assembly quality and efficiency.

Main Methods:

• For complete genomes, RFGR employs suffix trees to identify seed repeats with indels.
• For assembled genomes, RFGR utilizes a modified Bowtie aligner to find and extend exact repetitive sequences in contigs/scaffolds.
• For NGS reads, RFGR identifies and removes reads containing repetitive k-mers based on frequency.

Main Results:

• RFGR successfully identified thousands of repeats in control datasets (E. coli UTI89 and K12).
• Pre-processing E. coli K12 NGS data with RFGR led to a 22.86% improvement in N50 value and a ~50% reduction in assembly graph size.
• The tool achieved improved genome assembly with reduced computational requirements.

Conclusions:

• RFGR is an effective tool for identifying repetitive DNA sequences in prokaryotes, enhancing genome assembly.
• Future improvements could include finding approximate repeats, adjusting minimum repeat length, and extending applicability to eukaryotic genomes.