> For the complete documentation index, see [llms.txt](https://c-comp.gitbook.io/data-management-handbook/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://c-comp.gitbook.io/data-management-handbook/file-naming-conventions/sequencing-files.md).

# Sequencing Files

<figure><img src="/files/vc5198IaZlpp7fQkYl2k" alt=""><figcaption><p>This file name refers to the forward reads (R1) sequenced from a biological sample with the file number 8 that were collected using whole metagenomic sequencing in dataset CMP002.</p></figcaption></figure>

Please use this file naming template for raw sequences tool as a guide to create file names.

{% file src="/files/9FALS0kV4tQmPcVLEPXZ" %}

### **Field Definitions**

Each number in the example above corresponds to a field in the file name. Fields are separated by ‘\_’ to enhance computer readability. Shortened column names used in the template above are provided in parentheses next to the appropriate field definition.

1. Dataset Number (Dataset\_No):
   * All C-CoMP datasets will be assigned an internal dataset number. Please request this number on the #dataset\_number\_requests slack channel following the instructions provided above.
   * Metadata about the dataset (including Dataset number, method type, and data storage location) will be recorded in the C-CoMP Data Catalog.
2. Approach (Approach):
   * The kind of method that was used for this specific project X sample (see examples and abbreviations below)
3. Sample type (Sample\_Type):
   * Use this field to distinguish sample types. Sample type should fall into one of these categories: quality control (QC) or biological sample (SA). QC includes samples run as DNA extraction or sequencing controls to check for contamination during sample preparation.
4. File number (File\_No)
5. Forward or Reverse Reads (Forward\_Reverse):
   * Either the forward reads (R1) or reverse reads (R2) if applicable to the file type. Use ‘noR’ if this is not applicable.
6. Sequencing number (Seq\_no):
   1. Used if there is more sequencing data for the same sample and data type. This field is only changed if the sample is a technical replicate. If the sample is a biological replicate or from a separate extraction process, the sample is assigned  a different sample\_ID. Default number is 001.
7. File-type extension

**Approach Abbreviations:**

* WMX - Whole Metagenomic Sequencing (environmental metagenomics)
* WQX - Whole Genome Sequencing
* AMP - Amplicon Sequencing (e. g. 16S rRNA)
* TXX - Transcriptomics
* MTX - Environmental Metatranscriptomics

**Sample Type Abbreviations:**

* QC - Quality Control
* SA - Biological Sample


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