Simplifier: a web tool to eliminate redundant NGS contigs

Area of Science:

• Genomics
• Bioinformatics

Background:

• Modern genomic sequencing yields vast amounts of data but produces short reads.
• Short reads present challenges for genome assembly and resolving repetitive sequences.
• Post-assembly, curating numerous contigs requires substantial time and computational resources.

Purpose of the Study:

• To develop Simplifier, a stand-alone software for eliminating redundant sequences from assembled genomes.
• To reduce the manual effort and computational cost associated with genome assembly finalization.

Main Methods:

• Simplifier software was developed to selectively remove redundant sequences from contig collections.
• The software was tested on genome assembly data from Corynebacterium pseudotuberculosis and Escherichia coli.

Main Results:

• Simplifier reduced contigs by 34.14% (8,004 to 5,272) for C. pseudotuberculosis, increasing N50 from 1 kb to 1.5 kb.
• For E. coli, Simplifier processing reduced mate-paired library data by 17.47% and fragment library data by 23.91%.
• The software effectively removed redundant sequences, streamlining genome assembly.

Conclusions:

• Simplifier is an effective tool for reducing redundant sequences in genome assembly datasets.
• The software simplifies the finalization of genome assemblies, particularly for prokaryotic organisms.
• Simplifier saves considerable time and computational resources in genomic data analysis.