LongISLND: in silico sequencing of lengthy and noisy datatypes.
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.



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.
Roche Sequencing Solutions, Belmont, CA 94002, USA.
Bayo
B
Lau
Roche Sequencing Solutions, Belmont, CA 94002, USA.
Marghoob
M
Mohiyuddin
Roche Sequencing Solutions, Belmont, CA 94002, USA.
John C
JC
Mu
Roche Sequencing Solutions, Belmont, CA 94002, USA.
Li Tai
LT
Fang
Roche Sequencing Solutions, Belmont, CA 94002, USA.
Narges
N
Bani Asadi
Roche Sequencing Solutions, Pleasanton, CA 94588, USA.
Carolina
C
Dallett
Roche Sequencing Solutions, Belmont, CA 94002, USA.
Hugo Y K
HY
Lam
D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D016415:Sequence Alignment; D012984:Software
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