Bioinformatics Center
Services
Infrastructure
Guides
Hosted services
Bioinformatics Center
Services
Infrastructure
Guides
Hosted services
Solu (finnish word for Cell) computing server is meant for an interactive computing workloads. In addition to the traditional SSH terminal access the server provides graphical desktop environment that can be used with the Remote Desktop Connection Protocol.
Server address: solu.uef.fi
Server is connected to the storage space provided by the UEF IT Services for Research. More information can be found from the dedicated page.
URL: https://support.illumina.com/sequencing/sequencing_software/igenome.html
Following reference genomes can be found from the /apps/genomes/iGenomes folder.
Home sapiens | Version |
---|---|
GRCh37 | Ensembl |
GRCh38 | NCBI |
GRCh38Decoy | NCBI |
hg19 | UCSC |
hg39 | UCSC |
Mus musculus | Version |
---|---|
mm9 | UCSC |
mm10 | UCSC |
Rattus norvegicus | Version |
---|---|
rn4 | UCSC |
URL: https://gnomad.broadinstitute.org/downloads
Following variants can be found from the /apps/genomes/gnomAD folder.
Home sapiens | Version |
---|---|
Exome variants (.vcf.bgz) | gnomAD 2.1.1 / hg19 |
Genome variants (.vcf.bgz) | gnomAD 2.1.1 / hg19 |
System provides various graphical and terminal applications for the researchers.
Additionally to browser, office-suite and text editors the following graphical applications are available:
Graphical Applications | Version |
---|---|
MATLAB | R2018b |
RStudio | 3.5.1 |
RStudio | 3.6.0 |
RStudio-Server | 3.6.0 |
IGV | 2.5.2 |
Other Applications | Version | Address |
---|---|---|
Rstudio-Server | 3.6.0 | https://solu.uef.fi/rstudio |
Singularity Container | 3.2.1 |
In the terminal, you can see the list of available software packages by command 'modul avail'. A short list of available applications (19.06.2019) below:
homer/4.9.1 kallisto/0.43.1 seqan/2.4.0 bamtools/2.5.1 cufflinks/2.2.1 matlab/R2018b r/3.6.0 (L,D) bamutil/1.0.13 datamash/1.3 mono/5.4.1.7 samtools/1.9 bcftools/1.9 diamond/0.9.21 openmpi/1.10.7-2 star/2.5.1b bedtools2/2.27.1 fastqc/0.11.7 picard/2.18.3 star/2.5.4b bowtie/1.2 fastx-toolkit/0.0.14 plink/1.07 star/2.6.1b (D) bowtie2/2.3.4.1-python-3.7.0 gcc/8.2.0 prinseq-lite/0.20.4 tabix/2013-12-16 breakdancer/master hisat2/2.1.0 python/2.7.15 (L) trimmomatic/0.36 breakdancer/1.4.5 (D) htslib/1.9 python/3.7.0 vcftools/0.1.14 bwa/0.7.17 jdk/11.0.3 python/3.7.3 (D) clustalw/2.1 jdk/12.0.1 (L,D) r/3.5.1
Applications are managed with the Lmod Environment Module System. Guide for the Lmod can be found here
Available modules
module avail
Load module
module load bowtie2
If you wish to Load some specific version number
module load python/3.7.3
Unload module
module unload bowtie2
Save list of loaded modules
module save
Restore saved modules
module restore
You can quickly go to the application location by writing:
module load bowtie2 cd $BOWTIE2_ROOT