Bases2Fastq Workflow

The bases2fastq-nf workflow by Element Biosciences is a Nextflow workflow that generates FASTQ files from raw sequencing basecall data produced by AVITI Systems.

This workflow runs as part of ElemBio Cloud, but can also be used independently and reproducibly in any Nextflow environment (local or cloud-based).

Workflow Summary

Description

Converting .bases is the necessary first step to convert raw sequencing data to FASTQ file, the predominant file type required to begin secondary analysis. This single step pipeline uses the Bases2Fastq Software to demultiplex AVITI System data.

• Demultiplex reads and converts base calls into FASTQ files
• Optionally write index and UMI FASTQs
• Trim adapters before downstream analysis
• Generate a Bases2Fastq QC HTML report

Workflow Diagram

Release Notes

The workflow repository is maintained on GitHub, where you can find tags, release notes, and the latest updates.

Inputs

Bases2fastq-nf requires at minimum an AVITI sequencing run directory to run. Optional files may also be supplied.

Input	Description	Constraints
Run Directory	An AVITI System sequencing run directory.	Required
Sequencing Run Manifest	By default, the run manifest in the output run directory is used. If required, an alternate run manifest instead of the run manifest provided in the run directory.	Optional
Parameters	In addition to the dataset, parameters can tune the output.	Optional

Output

Bases2fastq-nf outputs the results of demultiplexing and the QC report. Depending on the parameters used, the output directory may be different. See Bases2Fastq outputs for specific details of output files.

Representative view of Bases2Fastq output

s3://output-bucket/analyses
└── bases2fastq
    └── wfr_671ae78b2d6a2fc62332f8a3
        ├── DVT-0274_QC.html
        ├── IndexAssignment.csv
        ├── Metrics.csv
        ├── RunManifest.csv
        ├── RunManifest.json
        ├── RunParameters.json
        ├── RunStats.json
        ├── Samples
        │   ├── DefaultProject
        │   │   ├── Sample_1
        │   │   │   ├── Sample_1_R1.fastq.gz
        │   │   │   ├── Sample_1_R2.fastq.gz
        │   │   │   └── Sample_1_stats.json
        │   │   ├── Sample_2
        │   │   │   ├── Sample_2_R1.fastq.gz
        │   │   │   ├── Sample_2_R2.fastq.gz
        │   │   │   └── Sample_2_stats.json
        │   │   ├── DefaultProject_Metrics.csv
        │   │   ├── DefaultProject_QC.html
        │   │   └── DefaultProject_RunStats.json
        │   └── Unassigned
        │       ├── Unassigned_R1.fastq.gz
        │       └── Unassigned_R2.fastq.gz
        ├── UnassignedSequences.csv
        ├── info
        │   ├── Bases2Fastq.log
        │   └── RunManifestErrors.json
        └── run.log

Input Parameters

Parameter	Type	Results
legacy_fastq	boolean	Applies the --legacy-fastq option.
detect_adapters	boolean	Applies the --detect-adapters option.
force_index_orientation	boolean	Applies the --force_index_orientation option.
split_lanes	boolean	Apples the --split_lanes option.
filter_mask	string	Applies the --filter-mask option with the supplied value.
flowcell_id	string	Applies the --flowcell-id option with the supplied value.
num_unassigned	integer	Applies the --num_unassiged option with the supplied value.
qc_only	string	Applies the --qc-only option; FASTQ files will not be generated
b2f_args	string	Send a string of arguments to Bases2Fastq. The string will be utilized as is. Recommended for local development only, advanced use cases, or test only.