PBSIM: PacBio reads simulator - toward accurate genome assembly

By Yukiteru Ono, Kiyoshi Asai, Michiaki Hamada. Bioinform., 2013

313 citations recorded by the source corpus.

Subfields: Catalysis, Inorganic Chemistry, Organic Chemistry

View Paper: https://www.semanticscholar.org/paper/4b28ac39da5af16f8f72582223783aae0333ec42

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Catalysis

1. Chong Chu
2. Heng Li
3. Xiaowen Feng

In Inorganic Chemistry

1. Chong Chu
2. Heng Li
3. Xiaowen Feng

In Organic Chemistry

1. Chong Chu
2. Heng Li
3. Xiaowen Feng

Citations in the corpus

• WhatsHap: fast and accurate read-based phasing (2016, methodology): “From those, we simulated reads that mimic the read length profile and coverage of the real data using pbsim [41].”
• Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads (2016, methodology): “For each short-read set, we used PBSIM[42] to generate synthetic long reads at seven depths (0.25x, 0.5x, 1.0x, 2.0x, 4.0x, 8.0x and 16.0x).”
• Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation (2016, background): “PacBio sequence lengths follow a log-normal distribution (Ono et al. 2013), and additional coverage increases the probability of spanning a long repeat.”
• Comprehensive evaluation of structural variation detection algorithms for whole genome sequencing (2019, methodology): “To generate a simulated dataset of long reads, PacBio long reads (average 7.5 – 20 kb) aimed at 10× coverage were simulated with Sim-A using the PBSIM simulator [57] (Fig.”
• The design and construction of reference pangenome graphs with minigraph (2020, methodology): “Ono, Y., Asai, K., Hamada, M.: PBSIM: PacBio reads simulator–toward accurate genome assembly.”
• One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly. (2015, background): “However, rapid advances in chemistry and library preparation have boosted both the median and maximum sequence lengths [18 ,33] to 10 kbp and 50 kbp respectively in the latest runs [36 ,37 ].”