Demultiplex: FASTA/FASTQ demultiplexer

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Versatile NGS demultiplexer with the following features:

• Support for FASTA and FASTQ files.
• Support for gzip and bzip2 compressed files.
• Support for multiple reads per fragment, e.g., paired-end.
• Handles barcodes in the header and in the reads.
• Handles barcodes at unknown locations in reads (e.g., PacBio or Nanopore barcodes).
• Support for selection of part of a barcode.
• Allows for mismatches, insertions and deletions.
• Barcode guessing by frequency or fixed amount.
• Handles large numbers (over one million) of barcodes.

Please see ReadTheDocs for the latest documentation.

Contents:

• Installation
  • From source
• Usage
  • Illumina FASTQ files
  • Other files
  • Multiple barcodes
  • Barcodes at unknown locations
• Command Line Interface
• Frequently asked questions
• Contributors