SPID documentation

Introduction

SPID stands for “Sequences with Polymorphic Indices Demultiplexer”

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

SPID 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.

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

The source code can be downloaded from https://bitbucket.org/incpm/spid-public

Why use SPID?

• Why Use SPID?
  • 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 SPID
  • BarcodeSheet
  • Usage examples
• Memory Usage
  • Memory usage explained
  • Examples

License

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

Authors

Refael Kohen,

refael.kohen@gmail.com

Ophir Tal,

ophir.tal@weizmann.ac.il

Ilana and Pascal Mantoux Institute for Bioinformatics, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 76100, Israel.