LongISLND: in silico sequencing of lengthy and noisy datatypes

Bayo Lau; Marghoob Mohiyuddin; John C Mu; Li Tai Fang; Narges Bani Asadi; Carolina Dallett; Hugo Y K Lam

doi:10.1093/bioinformatics/btw602

LongISLND: in silico sequencing of lengthy and noisy datatypes

Bioinformatics. 2016 Dec 15;32(24):3829-3832. doi: 10.1093/bioinformatics/btw602. Epub 2016 Sep 25.

Authors

Bayo Lau¹, Marghoob Mohiyuddin¹, John C Mu¹, Li Tai Fang¹, Narges Bani Asadi¹, Carolina Dallett², Hugo Y K Lam¹

Affiliations

¹ Roche Sequencing Solutions, Belmont, CA 94002, USA.
² Roche Sequencing Solutions, Pleasanton, CA 94588, USA.

Abstract

LongISLND is a software package designed to simulate sequencing data according to the characteristics of third generation, single-molecule sequencing technologies. The general software architecture is easily extendable, as demonstrated by the emulation of Pacific Biosciences (PacBio) multi-pass sequencing with P5 and P6 chemistries, producing data in FASTQ, H5, and the latest PacBio BAM format. We demonstrate its utility by downstream processing with consensus building and variant calling.

Availability and implementation: LongISLND is implemented in Java and available at http://bioinform.github.io/longislnd CONTACT: hugo.lam@roche.comSupplementary information: Supplementary data are available at Bioinformatics online.

MeSH terms

Computational Biology / methods*
Computer Simulation
High-Throughput Nucleotide Sequencing / methods*
Sequence Alignment
Software*