Sequencing > Genome Informatics


We provide collaborations and services related to genomic data analysis. Below is a short description of the most popular services we provde. Please e-mail us for additional or other requests.

Web-based NGS data analysis workflows

https://fgcz-sushi.uzh.ch provides access NGS data analysis apps where you can analyze your NGS data using the S3IT cloud infra-structure.
Available apps are listed at https://fgcz-sushi.uzh.ch/sushi_application . New apps will be added on request.
All analysis results are fully documented. All results are fully downloadable for further use.

Interactive plots and analyses

https://fgcz-shiny.uzh.ch lets you generate heatmaps, Venn diagrams, and other R-based visualization with a few clicks in your web-browser.
Additionally, you can interactively explore, filter and visualize your RNA-seq results generated with SUSHI.

RStudio for you

RStudio server — access to the server version of RStudio Lets you run R scripts on FGCZ hardware. Everything you need is a browser and a B-Fabric username/password.

Useful information:

• if you work in project p123, then all your NGS data is available at /srv/gstore4users/p123
• your home directory has a quota of max. 10GB. If you need more space, we will setup a larger folder for you at /srv/localdata/p123. Please note that this is intended for short term storage below 100GB. If you need bigger or long-term storage

e-mail us.

Server access

For commandline based analysis, you can access our user server with

ssh your_b-fabric_username@fgcz-genomics.uzh.ch

The file locations are

• data for project p123 is found at /srv/gstore4users/p123
• all software is at (more than 1000 commands available) /usr/local/ngseq/bin
• all reference genomes are found in /srv/GT/reference
• additional reference databases: /srv/GT/databases

This node is shared with other users. Be thoughtful with the use of resources. If you need more resources, please see the next section.

Virtual node for you

You can get access to a virtual node at the S3IT ScienceCloud where all NGS tools installed at FGCZ is available. Please follow the instructions for configuring a node on the science cloud

E-mail us for details and assistance.

Reference genomes and indices

https://fgcz-gstore.uzh.ch/reference holds reference genome sequences and indices for mappers for all genomes in use at the FGCZ. If you need an additional genome e-mail us

All genomes have a standard structure, e.g.:

Homo_sapiens
      Ensembl
        GRCh38
          Annotation
            Version-2015-07-05
              Genes
                genes.gtf
                genes_STARIndex
                genes_annotation.txt
          Sequence
            WholeGenomeFasta
               genome.fa
               genome.fa.fai
            Chromosomes
            BOWTIE2Index

Note: Indices for mappers are automatically created on demand.

We do keep different versions of the genomes and genome annotation. The version folders (e.g. https://fgcz-gstore.uzh.ch/reference/Homo_sapiens/Ensembl/GRCh38.PatchesSkipped/Annotation/Version-2015-07-05/ ) indicate the data the genome annotation was downloaded.
We do generate a reference genome folder from a gff/gtf file and a fasta file.

Submitting data to a public repository

We recommend submission to the ENA (European Nucleotide Archive) which is mirrored at the SRA (Short Read Archive). Instruction for submitting to ENA

Data storage policy

We keep secured and backup storage for

• 3 months for all data that is order as data delivery only.
• the run time of the project if we provide bioinformatics services for the projects

Storage extensions are subject to individual agreements.

Data access

instructions how to access data

ezRun

https://github.com/uzh/ezRun - our R package that holds convenience functions that we routinely use at the FGCZ.