Version

Bases2Fastq release notes

v3.0.0

October 19, 2026

Added support for Vitari™ sequencing runs. Vitari runs use the same commands and optional arguments as AVITI™ runs, and Bases2Fastq™ detects the instrument from RunParameters.json. FASTQ sequence identifiers for Vitari runs use 5-digit x and y coordinates.
Added the --unzip-to-disk optional argument to reduce memory use on Vitari runs by decompressing bases files to the temporary directory.
The HTML QC report is generated for cell screening runs in addition to sequencing runs. The report requires Python 3.8 or later and no additional Python packages.
Added the --bgzf-compression optional argument to write BGZF-compressed FASTQ files, each with a bgzip-compatible .gzi index file.
Added support for --filter-mask in cell screening runs. Masks are set per batch, such as B01:N5Y15N*-B02:YN*.
Added support for cell segmentation masks stored as Zarr v3 in --segmentation.
Each execution records started.json and completed.json files in the .attempts folder of the output directory. Bases2Fastq logs a warning when a local output directory contains a record from another execution.

Cell screening FASTQ sequence identifiers now include a trailing 7-digit polony index that resets for each z-tile. The field prevents duplicate read identifiers caused by negative x and y locations. Downstream parsers that split identifiers on : must expect the additional field.
Cell screening FASTQ sequence identifiers use a 10-digit cell ID instead of an 8-digit cell ID.
Combined-lane rows in Metrics.csv, IndexAssignment.csv, UnassignedSequences.csv, and project CSV files use the lane value All instead of 1+2. Downstream parsers that match 1+2 must expect All.
MultiQC reports are no longer generated. The --skip-multi-qc optional argument is removed. Remove --skip-multi-qc from your scripts.
Bases2Fastq logs a warning when a lane enables SpikeInAsUnassigned and specifies index sequences, because per-sample polony counts include spike-in polonies.
A failure to clean up remote scratch space logs a warning instead of stopping the execution.
FASTQ write error messages include the file path and the system error code.
The Docker image is based on Debian 13.

Resolved an issue where adapter trimming and statistics for DefaultSample included polonies that did not pass filter.
Resolved an issue where DefaultSample polony counts included spike-in polonies written to the Unassigned FASTQ files when SpikeInAsUnassigned is enabled.
Resolved an overflow in run-level polony counts for runs with more than about 4.29 billion polonies, which caused an incorrect PercentAssignedReads value.

May 27, 2026

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 --help output.
Added the --segmentation optional argument to pass in a directory of alternative cell segmentation masks when a new run segmentation mask is required.
Added the --force-detect-index-orientation optional 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.json reports it (available with AVITI OS 4.0.0 or later).
Added the --skip-empty-fq-files optional argument to suppress generation of empty FASTQ files for samples with zero reads.

Adapter trimming is now skipped for barcoding batches in cytoprofiling runs.
Increased the maximum length of RunValues entries 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 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.