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

LongISLND: in silico sequencing of lengthy and noisy datatypes

Bayo Lau  1 , Marghoob Mohiyuddin  1 , John C Mu  1 , Li Tai Fang  1 , Narges Bani Asadi  1 , Carolina Dallett  2 , Hugo Y K Lam  1
Affiliations

LongISLND: in silico sequencing of lengthy and noisy datatypes

Bayo Lau et al. Bioinformatics. .

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.

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Figures

Fig. 1.
Fig. 1.
(a) Number of 7-mers binned with respect to accuracy, determined within 1% as discussed in the Supplementary material. A context-independent error profile would yield a delta peaking function centered at the global accuracy. (b) Fraction of samples of a certain sequence length aligned to a homopolymer of true length 6. Compared to the analytical expression derived in the Supplementary Material, G/C deletion bias is observed in both P5 and P6 chemistries
See this image and copyright information in PMC

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