fastq-fix-i5

A fast, streaming tool to rewrite FASTQ headers by reverse-complementing the i5 (Index2 / P5) barcode, without modifying read sequences or quality scores.

Headers are expected to end with the standard Illumina :<i7>+<i5> format.

This tool can be useful when mixing FASTQs from different sequencing platforms (e.g. Illumina and AVITI) where i5 orientation conventions differ.

What this tool does

• Reads FASTQ from stdin
• Writes FASTQ to stdout
• For each record:
  • parses the FASTQ header
  • finds the final :<i7>+<i5> field
  • reverse-complements only the i5 part
• Leaves everything else unchanged

Installation

To install from bioconda:

conda install -c bioconda fastq-fix-i5

To build and install using the rust package manager cargo:

cargo install fastq-fix-i5

Alternatively you can download a pre-compiled binary for your platform.

Use

To run fastq-fix-i5, simply pipe your FASTQ data into it:

fastq-fix-i5 < input.fastq > output.fastq

If your input FASTQ is compressed, on linux you can use pigz to stream the data through fastq-fix-i5:

pigz -dc input.fastq.gz | fastq-fix-i5 | pigz -c > output.fastq.gz

Performance

fastq-fix-i5 is designed to be fast and memory-efficient. It processes FASTQ data in a streaming fashion, which allows it to process millions of reads per second using a single CPU core and <5MB of memory.