Please note before download:

To ensure that all files are downloaded correctly, we provide md5 checksums for the big files. Therefore after download, please verify the integrity of the downloaded file, i.e. whether it is complete and uncorrupted. To do so, you may use the md5 checksum provided (respective link). Search for 'md5 checksum' on the web to find suitable verification tools. Within the verification tool, browse and select the downloaded file and let the tool compute the checksum. If the two checksums differ, you have to download the file again.


Download from our ftp server:


All Genomes and SNP DBs available here can alternatively be downloaded from our ftp-server. We recommend to use the ftp server for the download of big files, because the download can be restarted in case there is an interruption.


  • You can reach the file server using the following link:
  • Please use the following login:

    Username: SeqPilotData

    Password: SeqPilot


Download from this website:



NOTE: The genome hg19 for download is only available for new installations. Please do not install genome hg19 in case it already exists in your installation.


NOTE: For hg19 and hg38 please decide which references (NCBI or ENSG) you want to use and download only one.


How to install a genome:

Close SeqPilot during installation. After download execute the file and follow the instructions to complete the installation.

As destination directory, select the directory GeneFiles of your SeqPilot installation (default: C:\SeqPilot\GeneFiles).


Download (hg19 for new installations only!):


for module SeqNext (or SeqPatient and SeqNext in one installation):

Name Genome Reference Size Checksum
hg19NCBI-SeqNext hg19 NCBI transcripts 3.43 GB hg19NCBI-SeqNext
hg19ENSG-SeqNext hg19 ENSG transcripts 3.43 GB hg19ENSG-SeqNext
hg38NCBI-SeqNext hg38 NCBI transcripts 3.43 GB hg38NCBI-SeqNext
hg38ENSG-SeqNext hg38 ENSG transcripts 3.44 GB hg38ENSG-SeqNext

for module SeqPatient:

Name Genome Reference Size Checksum
hg19NCBI-SeqPatient hg19 NCBI transcripts 719 MB hg19NCBI-SeqPatient
hg19ENSG-SeqPatient hg19 ENSG transcripts 727 MB hg19ENSG-SeqPatient
hg38NCBI-SeqPatient hg38 NCBI transcripts 725 MB hg38NCBI-SeqPatient
hg38ENSG-SeqPatient hg38 ENSG transcripts 733 MB hg38ENSG-SeqPatient



GenomeCompact for Genome Mapping (module SeqNext and software version 4.4.0 or higher only):

A genome mapping can be done to filter background/homologies. The genome mapping is recommended for big panels and enrichment panels. In case you want to use the genome mapping, the GenomeCompact files need to be downloaded:


Name Genome Size Checksum
hg19-GenomeCompact hg19 3.41 GB hg19-GenomeCompact
hg38-GenomeCompact hg38 3.43 GB hg38-GenomeCompact




Known Gene Lists (to update already existing Genomes):

We offer regular updates for the known gene lists including new transcripts from ENSEMBL or NCBI.


NOTE: Since existing transcripts might have changed all Panels/ROIs have to be set up new after updating your system! Please contact our support team in case you want to update the Known Genes: