Bases2Fastq release notes
v2.4.0
May 27, 2026
New Features
- Bases2Fastq binary distributions are now digitally signed with certificates to enhance software authenticity and protect against tampering.
- Introduced a Unique Device Identification (UDI) value shown in the
--helpoutput. - Added the
--segmentationoptional argument to pass in a directory of alternative cell segmentation masks when a new run segmentation mask is required. - Added the
--force-detect-index-orientationoptional argument, which uses all polonies, including those that do not pass filter, to detect index orientation. Use at your own discretion when no tile reaches the default 70% PF threshold during feature detection. - FASTQ headers now include the instrument model when
RunParameters.jsonreports it (available with AVITI™ OS 4.0.0 or later). - Added the
--skip-empty-fq-filesoptional argument to suppress generation of empty FASTQ files for samples with zero reads.
Improvements
- Adapter trimming is now skipped for barcoding batches in cytoprofiling runs.
- Increased the maximum length of
RunValuesentries in the run manifest from 255 to 16,384 characters to support longer input lists. - Added sorting by sample and by number of polonies to the Bases2Fastq HTML report.
Resolved Issues
- Resolved an issue where MultiQC reports omitted samples for runs producing large MultiQC inputs. The internal MultiQC file size limit has been raised from 50 MB to 500 MB.
- Resolved a Bases2Fastq HTML report display issue that caused polony numbers to wrap instead of displaying on one line.