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