PBSIM: PacBio reads simulator--toward accurate genome assembly

Area of Science:

• Genomics
• Bioinformatics

Background:

• PacBio sequencers generate two read types: continuous long reads (long, high error rate) and circular consensus sequencing (short, low error rate).
• Both read types are valuable for de novo genome assembly.
• A simulator specifically for PacBio read generation was lacking.

Purpose of the Study:

• To develop a simulator that accurately models PacBio read characteristics.
• To evaluate the performance of PacBio reads in hybrid error correction and genome assembly.

Main Methods:

• Analysis of 13 PacBio datasets to identify characteristic read features, such as log-normal distribution of read length.
• Development of PBSIM, a read simulator employing model-based and sampling-based methods.
• Conducting hybrid error correction and assembly tests using simulated PacBio reads.

Main Results:

• PBSIM successfully captures characteristic features of PacBio reads.
• Analysis revealed that a continuous long reads coverage depth of at least 15, combined with a circular consensus sequencing coverage depth of at least 30, is required for extensive genome assembly.
• PBSIM is available under the GNU GPL v2 license.

Conclusions:

• PBSIM is a valuable tool for simulating PacBio reads, aiding in genome assembly research.
• The study provides crucial insights into optimal coverage depths for different PacBio read types to achieve comprehensive genome assembly.