Bases2Fastq v1.4.0 Release Notes

The Bases2Fastq v_1.4.0 Software is now available. This version is required for all AVITI instrument runs performed on AVITI OS version 2.0.0 or later. Details of this release are described below.

New Features

  • The software now supports the output data type for AVITI OS 2.0.0. If you use AVITI OS version 2.0.0 or higher, upgrading to Bases2Fastq 1.4.0 is required to support the output data structure.
    • AVITI OS v2.0.0+ archives base calls files per cycle into a zip archive, reducing the total number of files output compared to previous AVITI OS versions.
    • AVITI OS 2.0.0 also introduces a new structure for input data files; run manifests no longer contain the [RunParameters] section, which are instead written to a RunParameters.json file.
    • Note: Bases2Fastq recognizes both data formats.
  • When the run manifest does not specify adapter sequences and adapter trimming is enabled, Bases2Fastq performs detection by default. Both R1 and R2 must have at least 48 cycles to leverage this feature. You can use the option --detect-adapters to override any sequences in the run manifest.


  • In addition to individual lanes, the Metrics.csv output file now reports the full run summary of both lanes (1+2).

Resolved Issues

  • When running Bases2Fastq in an Amazon EC2 instance with a detected IAM role as the credential, Bases2Fastq would fail to resolve the region due to an update to the Amazon region metadata. Bases2Fastq now supports AWS_REGION and AWS_DEFAULT_REGION. Role credential resolution within an EC2 instance will work as expected.
  • In the IndexAssignment.csv output file, the complete run yield is now reported instead of a single lane.
  • Color encoding in the console output is not compatible with some operating systems & terminals that do not display color. Instead of introducing additional dependencies, color encoding was removed to facilitate smoother pipeline experience for programmatic compute environments.
  • When one one of either read is greater than 48 cycles and the other read is less than 32 cycles and Paired-End type adapter trimming is used, bases2fastq would fail during execution. This is resolved.

Known Issues

None at this time.