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Future of Information and Communication Conference

FICC 2019: Advances in Information and Communication pp 326–340Cite as

Bioinformatics Tools for PacBio Sequenced Amplicon Data Pre-processing and Target Sequence Extraction

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Part of the book series: Lecture Notes in Networks and Systems ((LNNS,volume 70))

Abstract

Modern high throughput sequencing technologies are enormously contributing to the generation of heterogeneous genomic data of different sizes and kinds. In most of the cases, NGS data is first produced in the raw form, which is then demultiplexed into text based formats, representing nucleotide sequences i.e. FASTA and FASTQ formats for secondary analysis. One of the major challenges for the downstream analysis of amplicon data is to first demultiplex FASTQ files based on the different oligonucleotides barcode combinations. Match & Scratch Barcodes (MSB) are a set of interactive bioinformatics tools that support the analysis of PacBio sequenced long read amplicon data by detecting multiple forward and reverse end adapter sequences, generic adapters attached to the region specific oligoes, multiple number of region specific oligos of variable length for the extraction of sequences of interest. These work with zero mismatch, retain only reads which map exactly to adapters and barcodes, report all sequences matched to both single and paired-end adapters and barcodes, and demultiplex FASTQ files based on the common and distinct barcodes combinations. The performance of MSB has been successfully tested using in-house sequenced non-published and external published datasets, which includes PacBio sequenced long read PDX (Patient-Derived Xenograft) amplicon data embedding multiple barcodes of variable lengths. MSB is user friendly and first interactively designed set of tools to empower non-computational scientists to demultiplex their own datasets and export results in different data formats (CSV, FASTA and FASTQ).

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Acknowledgements

We thank Ahmed lab, Department of Genetics and Genome Sciences, Institute for Systems Genomics (ISG), School of Medicine, University of Connecticut Health Center (UConn Health), and The Jackson Laboratory for Genomics Medicine for their support to ZA, SZ and CYN. We also thank Partnership for Innovation and Education (PIE) and Technology Incubation Program (TIP) for supporting JP at UConn Health. We appreciate all colleagues, who have provided insight and expertise that greatly assisted the research and development.

Author information

Authors and Affiliations

  1. Genetics and Genome Science, School of Medicine, University of Connecticut Health Center (UConn Health), Farmington, CT, 06032, USA

    Zeeshan Ahmed & Justin Pranulis

  2. Institute for Systems Genomics, School of Medicine, University of Connecticut Health Center (UConn Health), Farmington, CT, 06032, USA

    Zeeshan Ahmed

  3. The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA

    Saman Zeeshan & Chew Yee Ngan

Authors
  1. Zeeshan Ahmed
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  2. Justin Pranulis
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  3. Saman Zeeshan
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  4. Chew Yee Ngan
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Corresponding author

Correspondence to Zeeshan Ahmed .

Editor information

Editors and Affiliations

  1. Faculty of Science and Engineering, Saga University, Saga, Japan

    Kohei Arai

  2. The Science and Information (SAI) Organization, Bradford, UK

    Rahul Bhatia

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Ahmed, Z., Pranulis, J., Zeeshan, S., Ngan, C.Y. (2020). Bioinformatics Tools for PacBio Sequenced Amplicon Data Pre-processing and Target Sequence Extraction. In: Arai, K., Bhatia, R. (eds) Advances in Information and Communication. FICC 2019. Lecture Notes in Networks and Systems, vol 70. Springer, Cham. https://doi.org/10.1007/978-3-030-12385-7_26

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