Genomes & SNP DBs

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: ftp://ftpsrv.jsi-medisys.de
  • Please use the following login:

    Username: SeqPilotData

    Password: SeqPilot

 

Download from this website:

 

Genomes:

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

 

 

SNP Databases:

An installation package including the databases dbSNP, 1000 Genomes, ClinVar, CLINVITAE and COSMIC is available for genomes hg19 and hg38 (for hg38 1000 Genomes is not available yet).

 

NOTE: These packages can only be installed in our software version 4.2.0 or higher.

 

NOTE: This package can be used for new installations as well as update for old installations.

 

NOTE: The database can only be used in case the genome hg19 or hg38 respectively is available in your SeqPilot installation.

 

How to install the SNP databases:

Update: Delete old database version first. Then proceed as explained for New installation below. Delete the folders containing the database information for the reference genome you want to replace. By default these are the following two folders of your SeqPilot installation (C:\SeqPilot):

  • For hg19: "GeneFiles\GenomeVar\hg19" and "GeneFiles\GenomeDBVar\hg19". Note: only delete the listed sub folders hg19 not the complete GeneFiles folder!
  • For hg38: "GeneFiles\GenomeVar\hg38" and "GeneFiles\GenomeDBVar\hg38". Note: only delete the listed sub folders hg38 not the complete GeneFiles folder!

New installation: unzip the file into the GeneFiles-directory of your SeqPilot installation (default: C:\SeqPilot\GeneFiles).

 

Download:

Genome Date Size Checksum
hg19-GenomeVarDB 19-March-2015 6.9 GB hg19-GenomeVarDB
hg38-GenomeVarDB 19-March-2015 3.9 GB hg38-GenomeVarDB

 

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: support@jsi-medisys.de.