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Inputs and Outputs

Input files for Bases2Fastq are the files output from a sequencing run. AVITI OS generates the files and transfers them to a run folder in your storage location.

During an execution, Bases2Fastq generates an output folder that contains the output files, an info directory, and a Samples directory. The Samples directory organizes FASTQ files and sample metrics into one folder for each sample. If the run manifest for the execution uses projects, the Samples directory creates one folder for each sample per project.

Example Output Directories​

With Project Folders​

The following file structure is a representative 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
│   │   ├── Project1_QC.html
│   │   ├── Project1_RunStats.json
│   │   ├── Project1_metrics.csv
│   │   ├── Project1_index_assignment.csv
│   │   ├── sample_0
│   │   │   ├── sample_0_R1.fastq.gz
│   │   │   ├── sample_0_R2.fastq.gz
│   │   │   └── sample_0_stats.json
│   │   ├── 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
│   ├── Project2
│   │   ├── Project2_QC.html
│   │   ├── Project2_RunStats.json
│   │   ├── Project2_metrics.csv
│   │   ├── Project2_index_assignment.csv
│   │   ├── sample_3
│   │   │   ├── sample_3_R1.fastq.gz
│   │   │   ├── sample_3_R2.fastq.gz
│   │   │   └── sample_3_stats.json
│   │   ├── sample_4
│   │   │   ├── sample_4_R1.fastq.gz
│   │   │   ├── sample_4_R2.fastq.gz
│   │   │   └── sample_4_stats.json
│   │   └── sample_5
│   │       ├── sample_5_R1.fastq.gz
│   │       ├── sample_5_R2.fastq.gz
│   │       └── sample_5_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 representative 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
│   │   ├── sample_0_R1.fastq.gz
│   │   ├── sample_0_R2.fastq.gz
│   │   └── sample_0_stats.json
│   ├── 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
│   ├── sample_3
│   │   ├── sample_3_R1.fastq.gz
│   │   ├── sample_3_R2.fastq.gz
│   │   └── sample_3_stats.json
│   └── sample_4
│       ├── sample_4_R1.fastq.gz
│       ├── sample_4_R2.fastq.gz
│       └── sample_4_stats.json
├── UnassignedSequences.csv
└── info
    ├── RunManifestErrors.json
    └── bases2fastq.log

Example Input Directory​

The following file structure is a representative example of an input directory. 

Example-Run-Directory
├── Alignment
│   └── L1R02C01S1
│       ├── R1_L1R01C01S1.aln
├── BaseCalls
│   └── L1R02C01S1
│       ├── I1_C001.zip
│       ├── I1_C002.zip
│       ├── I2_C001.zip
│       ├── I2_C002.zip
│       ├── R1_C001.zip
│       ├── R1_C002.zip
│       ├── R1_C003.zip
│       ├── R1_C004.zip
│       ├── R1_C005.zip
│       ├── ...
│       ├── R1_C151.zip
│       ├── R2_C001.zip
│       ├── R2_C002.zip
│       ├── R2_C003.zip
│       ├── R2_C004.zip
│       └── R2_C005.zip
│       ├── ...
│       ├── R2_C151.zip
├── Filter
│   ├── L1R02C01S1.filter
│   └── L1R02C01S2.filter
├── Location
│   ├── L1R02C01S1.loc
│   └── L1R02C01S2.loc
├── RunManifest.csv
├── RunManifest.json
└── RunParameters.json
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