16.2.22 Illumina sequencer run setup at the LSCF

Owned by Jordana Lindner
Last updated: 12 Nov, 2023 by Dena Leshkowitz
1 min read

From samples to sequencing output

The bioinformatics unit provides NGS setup and services that assist with retrieving raw fastq or demultiplexed files, and provide quality control measures for each sample that was sequenced.

Life Sciences Core Facilities (Sandbox) sequencing 

Weizmann users wishing to use the Institute's sequencers should coordinate a training session with Muriel Chemla, muriel.chemla@weizmann.ac.il.

Note that basic training / guidance is required, even for experienced users!

Trained users who wish to reserve sequencers can do so via Internal Services under ‘Advanced Sequencing Technologies (Sandbox)'.

In order to upload your sequencing data to the Illumina cloud services and get real-time remote monitoring, you may need to open an Illumina account.

For more details: https://www.weizmann.ac.il/LS_CoreFacilities/advanced-sequencing-technlogies/how-order


NGS Pipeline (SusanC) website

Once you start the run on the sequencer, wait 5 minutes and then log in to the NGS Pipeline (SusanC) website using your SusanC3 user id  and register the run. Make sure that you select the machine in which YOUR run had started.

In order to run analyses on the produced data, you will need to prepare a SampleSheet file with the details about your samples.

The file should be named and formatted according to the protocol you will be using.

For Tutorials and Instructions click here.

We recommend that you test your SampleSheet in advance. 

Once the run is finished, you will receive an email with a link to your data. For more information about the Workflow, see https://ngs-pipeline.weizmann.ac.il/ngsb/howto

Sequencing setup and Additional services for sequences

Getting your sequencing data

NGS setup and services: FAQ

UTAP requirements, setup, and reports


List of links 

Nextseq pipeline:

https://ngs-pipeline.weizmann.ac.il/

Help page:

https://ngs-pipeline.weizmann.ac.il/ngsb/howto

NGS pipeline.pptx

QC:

http://stefan.weizmann.ac.il/fqc/{type RUN ID here}, for example:

http://stefan.weizmann.ac.il/raw/180509_NB551168_0120_AHTKN2BGX5/

List of runs, with delete functionality:

https://ngs-pipeline.weizmann.ac.il/ngsb/storage


Bioinformatics support staff for UTAP: 

Visit our web site: http://www.weizmann.ac.il/LS_CoreFacilities/bioinformatics-lscf/about)