Simplifier

Simplifier eliminates redundant sequences from contig collections to reduce redundancy in ab initio genome assemblies and improve assembly metrics for prokaryotic genomes generated from short-read sequencing.

Key Features:

• Redundancy Elimination: Selectively eliminates redundant sequences from collections of contigs produced by ab initio genome assemblies.
• Assembly Efficiency: Reduces the number of contigs requiring downstream analysis and integration into complete genome sequences.
• Performance Metrics: In Corynebacterium pseudotuberculosis strain 258 reduced contigs from 8,004 to 5,272 (34.14%) and increased N50 from 1 kb to 1.5 kb; in Escherichia coli DH10B reduced mate-paired library contigs by 17.47% and fragment library contigs by 23.91%.
• Target Organisms: Tested on prokaryotic organisms for reducing effort in finalizing genome assemblies from short-read data.

Scientific Applications:

• Prokaryotic genome assembly: Facilitates reconstruction of complete prokaryotic genomes from fragmented sequences generated by short-read high-throughput sequencing.
• Post-assembly curation: Supports contig curation workflows and improvement of assembly metrics such as contig counts and N50 for mate-paired and fragment libraries.

Methodology:

Performs selective elimination of redundant sequences from contig collections produced by ab initio genome assemblies.