Automated finishing with autofinish.

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• Genome sequencing produces vast amounts of data, but the finishing process lags behind.
• Manual finishing decisions are time-consuming and hinder scalability.
• Automation is crucial to increase finishing rates and match shotgun sequencing output.

Purpose of the Study:

• To introduce and evaluate the Autofinish computer program for automating genome sequencing finishing.
• To compare the efficiency and effectiveness of an automated-hybrid finishing method against purely manual finishing.
• To assess the potential of Autofinish in reducing human intervention in genome finishing.

Main Methods:

• The Autofinish program automatically selects directed sequencing reads for genome project completion.
• An Autofinish-Hybrid method was compared to manual finishing across five diverse sequencing projects.
• Projects were finished using either Autofinish suggestions for the first three rounds or by a human finisher.

Main Results:

• The Autofinish-Hybrid method significantly reduced finishing time compared to human finishers alone.
• Both methods utilized a similar number and type of reads.
• Gap closure rates were comparable between the automated-hybrid and manual finishing approaches.
• Autofinish can handle various finishing strategies including resequencing, custom primer walks, and PCR.

Conclusions:

• Automating genome finishing with Autofinish offers substantial time savings.
• The Autofinish-Hybrid approach provides an efficient alternative to purely manual finishing.
• Autofinish is adaptable and has been successfully implemented in production at major sequencing centers for various applications.
• Recommends using Autofinish for initial rounds, with human intervention for complex cases.