Bioinformatics tools for pacbio sequenced amplicon data pre-processing and target sequence extraction

Zeeshan Ahmed, Justin Pranulis, Saman Zeeshan, Chew Yee Ngan

Research output: Chapter in Book/Report/Conference proceedingChapter


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).

Original languageEnglish (US)
Title of host publicationLecture Notes in Networks and Systems
Number of pages15
StatePublished - 2020
Externally publishedYes

Publication series

NameLecture Notes in Networks and Systems
ISSN (Print)2367-3370
ISSN (Electronic)2367-3389

All Science Journal Classification (ASJC) codes

  • Control and Systems Engineering
  • Signal Processing
  • Computer Networks and Communications


  • Amplicon data
  • Bioinformatics
  • PacBio
  • Software
  • Target sequences


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