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Overview of output directories

Input files for Bases2FastqDx are the files output from a run. AVITI Dx™ OS generates the input files and transfers them to a run folder in your storage location.

During an execution, Bases2FastqDx generates an output folder that contains the output files, an info folder, and a Samples folder. The Samples folder organizes FASTQ files and sample metrics into one subfolder for each sample. If the run manifest for the execution uses projects, the Samples folder creates one subfolder for each sample per project.

Example output directories for sequencing​

With project folders​

The following file structure is a example of an output directory when the run manifest groups samples into projects. Optional arguments can change the structure of output files.

output
├── 20230404-Bases2Fastq-Example-Run-QC.html
├── IndexAssignment.csv
├── Metrics.csv
├── RunManifest.csv
├── RunManifest.json
├── RunParameters.json
├── RunStats.json
├── Samples
│   ├── Project1 ... (for n projects)
│   │   ├── Project1_QC.html
│   │   ├── Project1_RunStats.json
│   │   ├── Project1_metrics.csv
│   │   ├── Project1_index_assignment.csv
│   │   ├── sample_0 ... (for n samples in the project)
│   │   │   ├── sample_0_R1.fastq.gz
│   │   │   ├── sample_0_R2.fastq.gz
│   │   │   └── sample_0_stats.json
│   ├── Project2
│   │   ├── Project2_QC.html
│   │   ├── Project2_RunStats.json
│   │   ├── Project2_metrics.csv
│   │   ├── Project2_index_assignment.csv
│   │   ├── sample_3 ... (for n samples in the project)
│   │   │   ├── sample_3_R1.fastq.gz
│   │   │   ├── sample_3_R2.fastq.gz
│   │   │   └── sample_3_stats.json
│   └── Unassigned
│       ├── Unassigned_R1.fastq.gz
│       └── Unassigned_R2.fastq.gz
├── UnassignedSequences.csv
└── info
    ├── RunManifestErrors.json
    └── bases2fastq.log

Without project folders​

The following file structure is a example of an output directory without projects. Optional arguments can change the structure of output files.

output
├── 20230404-Bases2Fastq-Example-Run-QC.html
├── IndexAssignment.csv
├── Metrics.csv
├── RunManifest.csv
├── RunManifest.json
├── RunParameters.json
├── RunStats.json
├── Samples
│   ├── Unassigned
│   │   ├── Unassigned_R1.fastq.gz
│   │   └── Unassigned_R2.fastq.gz
│   ├── sample_0 ... (for n samples in the project)
│   │   ├── sample_0_R1.fastq.gz
│   │   ├── sample_0_R2.fastq.gz
│   │   └── sample_0_stats.json
│   ├── sample_1 ...
├── UnassignedSequences.csv
└── info
    ├── RunManifestErrors.json
    └── bases2fastq.log

With grouped FASTQ files​

The following file structure is a example of an output directory when the execution uses the --group-fastq optional argument. Additional optional arguments can change the structure of output files.

output
├── 20230404-Bases2Fastq-Example-Run-QC.html
├── IndexAssignment.csv
├── Metrics.csv
├── RunManifest.csv
├── RunManifest.json
├── RunParameters.json
├── RunStats.json
├── Samples
│   ├── DefaultProject
│   │   ├── DefaultProject_IndexAssignment.csv
│   │   ├── DefaultProject_Metrics.csv
│   │   ├── DefaultProject_QC.html
│   │   ├── DefaultProject_RunStats.json
│   │   ├── sample_0_R1.fastq.gz ...(for n samples)
│   │   ├── sample_0_R2.fastq.gz ...(for n samples)
│   │   ├── sample_0_stats.json  ...(for n samples)
│   ├── Unassigned_R1.fastq.gz
│   └── Unassigned_R2.fastq.gz
├── UnassignedSequences.csv
└── info
    ├── RunManifestErrors.json
    └── bases2fastq.log

With grouped FASTQ files and no projects​

The following file structure is a example of an output directory when the execution uses the --group-fastq and --no-projects optional arguments. Additional optional arguments can change the structure of output files.

output
├── 20230404-Bases2Fastq-Example-Run-QC.html
├── IndexAssignment.csv
├── Metrics.csv
├── RunManifest.csv
├── RunManifest.json
├── RunParameters.json
├── RunStats.json
├── Samples
│   ├── sample_0_R1.fastq.gz ...(for n samples)
│   ├── sample_0_R2.fastq.gz ...(for n samples)
│   ├── sample_0_stats.json  ...(for n samples)
│   ├── Unassigned_R1.fastq.gz
│   └── Unassigned_R2.fastq.gz
├── UnassignedSequences.csv
└── info
    ├── RunManifestErrors.json
    └── bases2fastq.log

Example input directory for sequencing​

The following file structure is an example of an input directory for sequencing:

Example-Run-Directory
├── Alignment
│   └── L1R02C01S1
│       ├── R1_L1R01C01S1.aln
├── BaseCalls
│   └── L1R02C01S1 ...(for n tiles)
│       ├── I1_C001.zip ...(for n I1 cycles)
│       ├── I2_C001.zip ...(for n I2 cycles)
│       ├── R1_C001.zip ...(for n R1 cycles)
│       ├── R2_C001.zip ...(for n R2 cycles)
├── Filter
│   ├── L1R02C01S1.filter ...(for n tiles)
│   ├── L1R02C01S2.filter
├── Location
│   ├── L1R02C01S1.loc ...(for n tiles)
│   └── L1R02C01S2.loc
├── RunManifest.csv
├── RunManifest.json
└── RunParameters.json
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