Calculating Checksums

What is a Checksum?

A checksum (e.g., MD5 or SHA-256) is a fixed-length hash of a file's contents. If even a single byte changes during transfer, the checksum will be different — allowing you to detect corruption or incomplete uploads.

Generate a Checksum

macOS

# MD5
md5 filename.fastq.gz

# SHA-256
shasum -a 256 filename.fastq.gz

Linux

# MD5
md5sum filename.fastq.gz

# SHA-256
sha256sum filename.fastq.gz

Windows (PowerShell)

# MD5
Get-FileHash filename.fastq.gz -Algorithm MD5

# SHA-256
Get-FileHash filename.fastq.gz -Algorithm SHA256

Generate a Manifest File

For multiple files, generate a manifest listing checksums for all files in a directory:

# macOS / Linux — MD5 for all files in a folder
md5sum /path/to/data/* > data_manifest.md5

# Or SHA-256
sha256sum /path/to/data/* > data_manifest.sha256

Upload the manifest file alongside your data so the DMAC team can verify integrity on arrival.

Verify After Upload

After upload, re-run the checksum on the server and compare against your local manifest:

# Linux (on the server)
md5sum -c data_manifest.md5

Lines will show OK or FAILED. Re-upload any failed files.