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Inputs and Outputs

Input files for Bases2Fastq are the files output from a sequencing run. AVITI OS generates the input 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 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​

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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