IndeXeeker documentation

Introduction

IndeXeeker stands for “Index Seeker”

IndeXeeker is a software for demultiplexing FASTQ files based on tags (a.k.a barcodes) which are attached to each sequence.

IndeXeeker was planned to enable users to use with a wide range of tag types, and to mix samples with different tag types and different locations on the sequences, together in the same lane.

IndeXeeker reads multiplexed FASTQ files generated by bcl2fastq, Illumina’s base calling and demultiplexing software, and outputs demultiplexed FASTQ files in a similar format.

Why use IndeXeeker?

• Why Use IndeXeeker?
  • Features
    • Up to 3 tags for each sample
    • Tag position
    • Mismatches
    • Offsets
    • Wildcards
    • Switch reads
    • Per-sample parameters
  • Restrictions

Contents

• Installation
  • Install using pip
  • Get the code
  • Digging deeper
• Getting Started
  • Execution
  • The input files of IndeXeeker
  • BarcodeSheet
  • Usage examples
• Memory Usage
  • Memory usage explained
  • Examples

License

If not otherwise stated inside single files, IndeXeeker is licensed under GNU General Public License, version 3

Authors

Refael Kohen,

refael.kohen@gmail.com