Contact person
Szilárd Póliska
- E-mail: poliska@med.unideb.hu
- Phone: +36 52 411 717 /50216, 50210
1. Services
1. Storage and primary analysis of Illumina NGS data (e.g. QC and alignments). Our FTP server allows the downloading data in fastq, BAM and other files.
2. Providing access to the HPC (high performance computing) cluster for analysis and data storage. Data is stored in a redundant array of independent disks 6 (RAID6) configuration.
3. Reference genomes, bioinformatics programs, and pipe-lines for ChIP-seq, RNA-seq and ATAC-seq analyses are regularly up-dated by the staff.
4. Complex analyses of RNA-seq data: QC, identification of differentially expressed genes, statistical and pathway analyses, data visualization for collaborators.
5. Organizing courses, operating LIMS system, providing data analyses in large projects as members of Consortiums.
2. Key parameters of the HPC cluster
2.1. External storage with app. 100 TB capacity in RAID6 configuration
2.2. Fatnodes and compute nodes
- Head (admin) node - CPU: 44, memory: 126 GB
- n001, n002, n003, n004, n005, n006 CPU: 12, memory: 46 GB
- n007 - CPU: 44, memory: 251 GB
- n008 - CPU: 12, memory: 142 Gb
- n009 - CPU: 12, memory: 125Gb
3. Genomes and Key programs
3.1. Genomes
Mus musculus: mm9, mm10
Homo sapiens: hg18, hg19
Rattus norvegicus: rn4
Saccharomyces cerevisiae: S288c
Vitis vinifera: Vit.vin.GCA_000003745.2
Prunus persica: Pru.per.GCA_000346465.1
Malus domestica: Mal.dom.GCF_000148765.1
Solanum lycopersicum: Sol.lyc.SL2.50
Nicotiana benthamiana: Nic.ben.v1.0.1
3.2. Key programs
/data2/programs/tophat-2.1.1.Linux_x86_64/tophat
/data2/programs/cufflinks-2.2.1.Linux_x86_64
/data2/programs/bowtie2-2.2.8
/data2/programs/maker/bin/maker
/molbio/bin/RNA-seq_dj-ah/RNA-seq_main_v3-2.sh
/molbio/bin/ChIP-seq/ChIP-seq_anal-v1_9.sh
/data2/programs/bcftools/bcftools-1.3 - Tools for variant calling and manipulating VCFs and BCFs
/data2/programs/bwa/bwa-0.7.12/ – alignment via Burrows-Wheeler transformation
/data2/programs/impute_v2.3.2 – imputation tool
/data2/programs/R-3.2.3/
/data2/programs/tophat-2.1.1 TopHat maps short sequences from spliced transcripts to whole genomes