Asst Prof Dr Zeeshan AHMED edited this page Mar 22, 2018 · 13 revisions

Welcome to the Match & Scratch Barcodes wiki!

A set of interactive and cross-platform bioinformatics tools for the Extraction of Target Sequences from PacBio and Illumina Amplicon Data. It is implemented in JAVA programming language to meet the research aims and developmental objective of this study. Here, we explain the graphical user interface of Match & Scratch Barcodes with available features.

msb_main

1. Match Barcodes (MB)

MB provide following features:

  • Adding forward and reverse adapter sequences at the start and end of sequence

  • Adding multiple (comma separated) forward and reverse barcodes, at the start and end of sequence

  • Loading FASTQ file (input, amplicon data)

  • Count input adapter sequences and barcodes

  • Consider complete or specific regions for analysis by setting maximum start and end base pairs limit for the forward and reverse directions

  • Calculate false-positive and actual positive number

  • Press “Start Analysis” button to filter out:

    • a. mismatched sequences
    • b. matched sequences to any of the input sequence adapters
    • c. matched sequences to the paired end sequence adapters
    • d. matched sequences to any of the input barcode
    • e. matched sequences to paired sequence barcodes
    • f. Combinations of extracted sequences based on common and distinct barcodes.
  • Demultiplex target regions in one or multiple files in following formats:

    • a. “CSV”,
    • b. “FASTA” (single-line description starting with a “>” sign, followed by one/multiple lines of sequence data),
    • c. “FASTQ” (structure based one/multiple sets of four lines: first begins with “@” sign and third with “+” sign and both are for optional description, second contains nucleotide sequence and fourth comprises of ASCII encoded Phred quality score for each nucleotide).

2. Scratch Barcodes (SB)

  • SB provide following features:
  • Read any number of FASTQ files as input
  • Match maximum four combinations of sequence adapters.
  • Directly match sequences as well as match in an order,
  • It matches first set of combinations with reads and matches second with only mismatched reads and accordingly for subsequent others.
  • Allows user to
    • a. add adapter sequences,
    • b. load FASTQ files,
    • c. analyze and report results:
      • i. total number of reads,
      • ii. total mismatched reads,
      • iii. matched reads with all four sequence adapters
      • d. export results in “CSV” format.

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