> For the complete documentation index, see [llms.txt](https://docs.hits.ai/omicshorizon-user-guide-en/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.hits.ai/omicshorizon-user-guide-en/project/recommended-file-formats-for-upload.md).

# Recommended file formats for upload

For analysis, we recommend uploading files in the format below, but files not specified may also be uploaded.

### 1. Sequencing Raw / Processed Data

| Format | Extension               | Description                  |
| ------ | ----------------------- | ---------------------------- |
| FASTQ  | .fastq, .fq, .fastq.gz  | NGS raw reads                |
| FASTA  | .fasta, .fa, .fna, .faa | Sequence reference / results |
| BAM    | .bam                    | Aligned reads (binary)       |
| SAM    | .sam                    | Aligned reads (text)         |
| CRAM   | .cram                   | Compressed alignment         |
| SRA    | .sra                    | NCBI SRA archive             |

### **2. Variant / Genomic Analysis**

| Format    | Extension         | Description              |
| --------- | ----------------- | ------------------------ |
| VCF       | .vcf, .vcf.gz     | Variant calling results  |
| BCF       | .bcf              | Binary VCF               |
| BED       | .bed              | Genomic intervals        |
| GFF / GTF | .gff, .gff3, .gtf | Gene annotations         |
| BigWig    | .bw, .bigwig      | Coverage / signal tracks |
| Wiggle    | .wig              | Coverage data            |

### **3. Transcriptomics / Expression Data**

| Format       | Extension        | Description                  |
| ------------ | ---------------- | ---------------------------- |
| Count Matrix | .tsv, .csv, .txt | Expression matrix            |
| H5AD         | .h5ad            | Single-cell (AnnData)        |
| MTX          | .mtx             | Sparse matrix (10x Genomics) |
| Loom         | .loom            | Single-cell data             |
| RDS          | .rds             | R Seurat object              |
| CEL          | .cel             | Affymetrix microarray        |

### **4. Proteomics / Metabolomics**

| Format | Extension | Description                         |
| ------ | --------- | ----------------------------------- |
| mzML   | .mzml     | Mass spectrometry standard          |
| mzXML  | .mzxml    | Mass spectrometry (legacy)          |
| MGF    | .mgf      | Peak lists                          |
| PDB    | .pdb      | Protein structure                   |
| mmCIF  | .cif      | Protein structure (modern standard) |

### **5. General / Metadata**

| Format | Extension         | Description                         |
| ------ | ----------------- | ----------------------------------- |
| Tables | .csv, .tsv, .xlsx | Sample metadata, results            |
| JSON   | .json             | Configuration, pipeline definitions |
| YAML   | .yaml, .yml       | Configuration files                 |
| PDF    | .pdf              | Reports                             |

### **6. Index / Auxiliary Files**

| Format      | Extension | Description     |
| ----------- | --------- | --------------- |
| BAM Index   | .bai      | BAM index       |
| FASTA Index | .fai      | FASTA index     |
| Tabix Index | .tbi      | VCF / BED index |