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Release Notes

November 20, 2023​

Bases2Fastq v1.6.0

Improvements​

  • To support the Individually Addressable Lanes add-on, the automatic detection for adapter trimming supports samples from each lane.

Resolved Issues​

  • If Bases2Fastq exceeds local disk memory during an execution, the execution stops and displays a warning message rather than truncating FASTQ files or ending unexpectedly.
  • Bases2Fastq identifies + and - as adapter sequence delimiters rather than causing an error.

September 6, 2023​

Bases2Fastq v1.5.1

New Features​

None

Resolved Issues​

  • When you specify the --filter-mask option with the --qc-only or --demux-only optional parameters, the software successfully applies the custom filter mask to the output dataset, rather than failing to apply the options.

  • When you specify the --filter-mask option with no cycles for a single read (e.g., R1:Y15N*-R2:N*), the software correctly interprets the basemask and uses it during execution, rather than the execution failing.

August 14, 2023​

Bases2Fastq v1.5.0

The Bases2Fastq v1.5.0 Software is available.

New Features​

  • Projects are introduced to group sample analyses. Projects are defined per sample in Sample Custom Metadata columns in the Run Manifest.
    • Within each project directory, a {ProjectName}_RunStats.json file and an HTML QC report are available for each project and use project-aggregated samples. Project-level files exclude run-specific values.
    • The default directory structure has changed. The default directory structure includes project folders that group samples. Use the --no-projects optional argument to retain the original output directory structure.
  • For Cloudbreak chemistry sequencing runs, you can customize the filter mask with the --filter-mask options to adjust which reads pass filter during base calling.

Resolved Issues​

  • If one read is greater than 48 cycles, the other read is less than 32 cycles, and paired-end adapter trimming is used, Bases2Fastq fails during execution. If cycle constraints are violated for the selected adapter trimming type, an error correctly displays.

Known Issues​

  • When you specify the --filter-mask option with the --qc-only or --demux-only optional parameters, the software fails to apply the custom filter mask to the output dataset.
  • When you specify the --filter-mask option with no cycles for a single read (e.g., R1:Y15N*-R2:N*), the execution fails.

April 27, 2023​

Bases2Fastq v1.4.0

The Bases2Fastq v1.4.0 Software is available. This version is required for all AVITI instrument runs performed on AVITI OS v2.0.0 or later.

New Features​

  • The software supports the output data type for AVITI OS v2.0.0. If you use AVITI OS v2.0.0 or higher, upgrading to Bases2Fastq v1.4.0 is required to support the output data structure.
    • AVITI OS v2.0.0 or later 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 v2.0.0 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.
    • 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.

Improvements​

  • In addition to individual lanes, the Metrics.csv output file 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 supports AWS_REGION and AWS_DEFAULT_REGION. Role credential resolution within an EC2 instance works as expected, rather than Bases2Fastq failing to resolve the region due to an update to the Amazon region metadata.
  • The IndexAssignment.csv output file reports the complete run yield, rather than a single lane yield.
  • Color encoding in the console output is not compatible with some operating systems and terminals that do not display color. Instead of introducing additional dependencies, color encoding is no longer used to facilitate a smoother pipeline experience for programmatic compute environments.

Known Issues​

  • If one read is greater than 48 cycles, the other read is less than 32 cycles, and paired-end adapter trimming is used, Bases2Fastq fails during execution. As a workaround, single-end type adapter trimming can be used instead.

Oct 20, 2022​

Bases2Fastq v1.3.0

New Features​

  • The software detects the orientation of index sequences during demultiplexing instead of using the orientation specified in RunManifest.csv. If the detected orientation differs from the run manifest, the statistics output file indicates the detection. This feature creates a more robust method of demultiplexing by reducing user errors.
  • A new statistics file, IndexingAssignment.csv, reports the indexing metrics for each sample pair.
  • A new optional argument, qc-only, reports statistics without generating any FASTQ files.
  • The software supports rclone, a command-line program that manages files in cloud storage, as input and output remotes to interact with cloud storage from various providers. Element has not tested all rclone configurations.

Resolved Issues​

  • To optimize download time when executing Bases2Fastq on a subset of data, only the subset data that option filters provide is downloaded, rather than the complete dataset.
  • If RunParameters.json is missing FlowCellID, Bases2Fastq reverts to using the RunID as the flow cell identifier to prevent blanks in FASTQ headers and unidentified flow cells.
  • If RunParameters.json is missing RunName, Bases2Fastq reverts to using the RunID as the run name to prevent blanks in FASTQ headers.
  • If whitespace was added to any fields in the FASTQ header, the whitespace is trimmed to prevent processing errors in the FASTQ headers.

Known Issues​

  • If one read is greater than 48 cycles, the other read is less than 32 cycles, and paired-end adapter trimming is used, Bases2Fastq fails during execution. As a workaround, single-end type adapter trimming can be used instead.
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