Naming Conventions

CBIcall supports both Illumina-style FASTQ names and run accession-based FASTQ names used in public datasets such as 1000 Genomes, ENA, and SRA.

Main rule

For active WES/WGS single-sample workflows, paired FASTQs must be matchable as _R1_ and _R2_, and all FASTQs for the sample should live in the same sample directory.

The FASTQ filename does not need to contain the sample ID, _ex, or _wg as long as mate pairing is unambiguous.

What CBIcall Uses

Item	Required?	Why it matters
_R1_ / _R2_ in FASTQ names	Yes	Used to pair reads.
One sample per sample directory	Yes	The sample directory defines the analysis unit.
Sample ID inside FASTQ filename	No	Useful for humans, but not required by current single-sample workflows.
_ex / _wg suffix	Legacy-dependent	Useful for older CNAG layouts, GATK 3.5, and mtDNA workflows.

Supported FASTQ Styles

Illumina-Style Names

NA12878_S1_L001_R1_001.fastq.gz
NA12878_S1_L001_R2_001.fastq.gz

This is the standard pattern for many local sequencing runs.

Run Accession-Based Names

HG00096/
├── ERR3239276_S1_L001_R1_001.fastq.gz
├── ERR3239276_S1_L001_R2_001.fastq.gz
├── ERR3239277_S1_L002_R1_001.fastq.gz
└── ERR3239277_S1_L002_R2_001.fastq.gz

Here, the FASTQ prefix is the run accession. The sample is defined by the directory, not by the FASTQ basename.

Legacy _ex / _wg Layout

Keep the historical _ex / _wg convention when a project may use:

• GATK 3.5 workflows
• MToolBox / mtDNA workflows
• older CNAG run layouts

Directory convention

In legacy-compatible layouts, the sample directory name is more important than the FASTQ filename itself.

Project directory:

CN99999_exome

Sample directory:

CN9999901P_ex

Part	Meaning
CN99999	Family or project identifier.
01	Individual/sample index within the project convention.
P	Role code, for example proband/patient.
_ex	Exome sample directory suffix.

Common role codes:

Code	Meaning
P	Proband / patient
F	Father
M	Mother

Legacy-compatible layout:

CN99999_exome/
└── CN9999901P_ex/
    ├── CN9999901P_ex_S1_L001_R1_001.fastq.gz
    └── CN9999901P_ex_S1_L001_R2_001.fastq.gz

The same layout also works with run-based FASTQ names:

CN99999_exome/
└── CN9999901P_ex/
    ├── ERR3239276_S1_L001_R1_001.fastq.gz
    ├── ERR3239276_S1_L001_R2_001.fastq.gz
    ├── ERR3239277_S1_L002_R1_001.fastq.gz
    └── ERR3239277_S1_L002_R2_001.fastq.gz

Equivalent Examples

For current single-sample WES/WGS workflows, both examples are valid:

CNAG99901P_ex_S2_L001_R1_001.fastq.gz
CNAG99901P_S2_L001_R1_001.fastq.gz

What matters is that the matching mate exists as _R2_ and that all FASTQs for the sample are grouped together.

Next Steps

• Build a YAML file with Configuration Reference.
• Run a test with Quickstart.
• Inspect generated files with Outputs.