We are a full service facility and provide consultation, instrumentation, and analysis services to both Penn State and non-Penn State investigators in various genomics projects.
Available instruments:
1. Nucleic acid processing and analysis
• QIAsymphony
• Bullet Blender
• Covaris (adaptive focused acoustics ultrasonicator E-series)
• 2 Bioanalyzers
• Nanodrop
• Qubit
• access to a TapeStation
• access to a Molecular Devices FlexStation 3 UV/Vis/Fluor spectrophotometer
• QuantStudio 12K Flex system with robotic plate handler
• QuantStudio 3D digital PCR
• access to Thermo Fisher 3500 Genetic Analyzer (Sanger sequencing)
• 10X Genomics Chromium
• Fluidigm C1 Single-Cell Auto Prep System
• access to a NanoString nCounter (PSU University Park campus)
2. Microarray
• Illumina microarrays with iScan system
• access to an Affymetrix (PSU University Park campus)
3. Next Generation Sequencing platforms
• Illumina 2 MiSeqs
• Illumina NovaSeq 6000
• LifeTech Ion Proton
4. 3rd Generation Sequencing platforms
• access to a PacBio Sequel (PSU University Park campus)
• BioNano Saphyr
• Oxford Nanopore Technologies MinION
Example Services and Costs
(CAUTION! below is outdated/not our official prices as of 2020) We provide cost estimates at the consultation or prior to the sample submission. The actual bill may come out slightly different but Director will supplement such information as project progresses)
1) DNAseq (mutation finding, assembly)
a) Whole genome sequencing (mammalian genome): $1,200 (30X coverage) –
b) Exome-Sequencing analysis (human whole exome): $340 (30X coverage, 10% duplicates) ~ $670 (80X coverage, 20% duplicates)
c) Exome-Sequencing analysis (targeted gene panel): please inquire
d) BioNano Irys whole genome mapping: please inquire
2) RNAseq
a) polyA-RNA: $250
b) total (rRNA depleted) RNA: $280
c) 3’mRNAseq (QuantSeq): $95
d) small (micro) RNA: $165
e) low input RNA: $300
f) direct RNA-seq by Oxford Nanopore MinION: please inquire
3) exRNAseq
a) exosome purification: $18
b) small (micro) RNA-seq (including RNA extraction from exosome): $180
4) single cell genomics
a) Fluidigm 96 cells or 800 cells RNAseq: please inquire
b) 10X Chromium ~10K cells RNAseq, ATACseq, immune profiling, surafce protein: please inquire
c) 10X Visium spacial transcriptome: please inquire
5) ChIPseq (ChIP’ing service is not available)
a) Histone marks: $250
b) Transcription factor: $160
6) DNA methylation
a) RRBS: $295
b) whole genome: please inquire
c) targeted: please inquire
7) Metagenome
a) 16S-seq: please inquire
b) shotgun whole genome sequencing: $370~ (please inquire)
c) whole metatranscriptome sequencing: $300~ (please inquire)
8) Microarray
a) SNP genotyping, CNV analysis: $70-$370 (minimum sample number required, please inquire)
b) methylation: $365 (minimum sample number required, please inquire)
c) gene expression: $117~ (minimum sample number required, please inquire)
9) qPCR (machine usage, please inquire for options of sample prep/assay design)
a) QuantStudio 12K Flex, 96 and 384 well (small-scale project): $20 per plate run
b) OpenArray (mid-scale project): please inquire
c) QuanStudio 3D digital PCR: $10.5
10) Bioinformatics
The College of Medicine has a dedicated HPC environment on campus with a total of:
• 336 CPU Cores (672 Threads)
• 21504 NVIDIA CUDA Cores (6 Tesla P100 GPUs with 16 Gigabytes RAM and 3584 NVIDIA CUDA cores each)
• 4864 Gigabytes of RAM
• 2 Petabytes of Total Storage Space
• 100 Terabytes of High Speed Scratch Space
• 1900 Terabytes of Usable Storage
• Storage is attached to a 10 Gigabit network backbone
Specifications
• 3x Dell R730 compute nodes with 768 Gigabytes of RAM each with 32 cores (64 threads) 2.30 GHZ and 2 NVIDIA Tesla P100s (16 Gigabytes RAM and 3584 NVIDIA CUDA cores each)
• 10X Dell R630 compute nodes with 256 Gigabytes of RAM each with 24 cores (48 threads) 2.5 GHZ
• 3x Dell R430 gateway nodes with 128 Gigabytes of RAM each with 16 cores (32 threads) 2.4GHZ
• 2 Petabytes Nexenta Enterprise Level Storage.
The Penn State College of Medicine Research Informatics group (http://med.psu.edu/core/informatics) is available for full support of the operation and maintenance of the HPC system. As of October 2018, below softwares are installed and maintained to support various sequence analysis including variant identification, transcriptome quantification, epigenetic profiling, de novo assembly, as well as statistical analysis correlating genomic with phenotypic information.
abruijn/2.1b cutadapt/1.9.1_py2.7.9 HiCExplorer/1.3 opencv/3.3.0 rMATS/4.0.0
abyss/1.35 debarcer/0.3.1 hiclib/0.0.0_2.7.11 OpenFOAM/v1706 RNA-SeQC/1.1.8
abyss/1.52 debarcer/2.0.1a HINGE/0.5.0 openmpi/1.10.1 rover/2.0.0
abyss/1.9.0 delly/0.7.3 hisat2/2.1.0 openmpi/3.0.1 rsem/1.2.28
allpathslg/52488 dietnet/0.1 homer/4.8 openmpi/3.1.2 RSEM/1.3.0
amos/3.1.0 DNMFilter/0.1.1 htseq/0.6.1 openmpi/default rstudio/0.98.1103
AmpliconNoise/1.29 dxchange/0.1.3 htslib/0.2.0 pandaseq/2.8.1 rtax/0.984
anno/2.13 EgaCryptor/0.2.25 htslib/1.2.1 parallel/159022 runes/4.2.1
annovar/2015-12-14 EGADemoClient/2.2.2 htslib/1.3.0 ParaView/v5.4.1 sailfish/0.10.0
apache-ant/1.9.7 emacs/24.5 htslib/1.6.0 pathscan/0.0.1 salmon/0.7.2
apache-commons-math3/3.6.1 eman/1.9 htslib/1.8.0 patterncnv/1.0 sambamba/0.6.7
aria2/1.33.1 eman2/2.12 hunspell/1.6.2 pBWA/1.21009 samblaster/0.1.24
athlates/1.0.0 eman2/2.2 iadmix/v0.2 pcre/8.41 samtools/0.1.19
auto3dem/4.05.2 eman2/2.21 ICA_AROMA/0.4.4 pear/0.9.6 samtools/1.2.0
autoconf/2.69 eman-cluster/1.9 iced/0.3.0 peet/1.12.0 samtools/1.3.0
automake/1.16.1 ensembl-api/02082016 imod/4.9.10 percolator/2.10.0 samtools/1.6.0
bamtools/2.3.0 ensembl-git-tools/12182013 imod/4.9.6 perl_list_util/1.43 samtools/1.8.0
bamtools/2.4.0 fastq/05272014 infernal/1.0.2 picard/1.102 sas/9.4
barracuda/0.7.0 fastqc/0.11.2 infernal/1.1.1 picard/1.141 SeqPrep/1.1
bazel/0.4.5 fastqc/0.11.4 IQSeq/2014 picard/2.0.1 seqtk/1.0-r82
bbmap/36_49 fastQValidator/0.1.1a java/1.8.0_65 pindel/0.2.5b8 snap/0.15.4
bcbio-nextgen/0.9.6 fastQValidator/0.1.rc012016 jdk/1.8.0_65 platanus/1.2.4 snap/1.0beta.23
bcbio-variation/0.2.6 fastx_toolkit/0.0.13 jellyfish/1.1.11 platypus/0.8.1 snappy/1.1.7
bcftools/0.2.0 fastx_toolkit/0.0.14 jellyfish/2.2.5 plink/1.07 snpEff/4.2
bcftools/1.3.0 FFmpeg/3.1.11 jgi_itagger/0.01 plink/1.90b3.30 SOAPdenovo2/r240
bcl2fastq/1.8.4 fftw/3.3.6 juicer/1.7.5_cuda8 plinkseq/0.10 somatic-sniper/1.0.5.0
bcl2fastq/2.18.0.12 fiji/1.50g juicer/1.8.9_cuda8 polymutt/0.18 sourcetracker/0.9.8
bcl2fastq/2.19.0.316 FineSplice/0.2.2 keras/2.0.8 polymutt2/0.2 Specter/1.0SA
bcl2fastq/2.20.0.422 fltk/1.3.4-2 kraken/0.10.5 polysolver/1.0 sratoolkit/2.5.7
bedtools/2.25.0 fqextract/110803 lachesis/1.0 pplacer/1.1.alpha19 sratoolkit/2.8.0
bioperl/1.6.924 freebayes/0.9.14 last/926 primer3/2.4.0 sratoolkit/2.9.2
Bio-Samtools/1.43 freebayes/1.0.2 leveldb/1.20 prinseq-lite/0.20.3 sRNAtoolboxDB/1.0
bismark/0.17.0 freesurfer/6.0.0 libgpuarray/v0.6.2 prinseq-lite/0.20.4 STAR/2.5.3a
blast/2.2.22 FSL/5.0.11 libgpuarray/v0.6.2_gcc5.3.0 protobuf/3.0.2 subread/1.6.2
blast/2.2.26 gatk/2.6.5 libgtextutils/0.7 python/2.7.11 surpi/1.0.18
blast+/2.2.31 gatk/2.7.4 libstatgen/1.0.14 python/2.7.11.ucs4 svtoolkit/2.00.1685
blast+/2.4.0 gatk/3.3.0 LMDB/0.9.21 python/2.7.14 tensorflow/1.3.1
blast+/2.7.1 gatk/3.5 lumpy-sv/0.2.3 python/2.7.6 tomopy/1.0.0
blat/35 gatk/3.8.0 macs/1.4.2 python/2.7.9 tophat/2.1.1
blat/36 gatk/4.0.2.1 macs2/2.1.0 python/3.6.0 torchvision/0.1.9
boost/1.59.0 Gautomatch/0.53 macs2/2.1.1 python/3.6.0_shared torchvision/2.0.ucs2
boost/1.63.0 Gautomatch/0.56 mafft/7.273 pytorch/0.4.1_cuda9.1.85 TransDecoder/5.0.2
boost/1.66.0 gcc/4.7.4 mageck/0.5.6 qiime/1.9.1_py2.7.11 trimmomatic/0.35
bowtie/1.1.2 gcc/4.9.3 manta/1.3.2 qiime/1.9.1_py2.7.6 trinity/2.1.1
bowtie2/2.2.4 gcc/5.2.0 matlab/R2018a qiime/1.9.1_py2.7.9 trinity/2.5.1
bowtie2/2.2.6 gcc/5.3.0 MCR/2016a qiime2/2017.10 trinity/2.5.1R
bwa/0.5.9 Gctf/1.06 Meerkat/0.189 QoRTs/1.3.0 TrioDeNovo/0.04
bwa/0.6.2 Gctf/1.18 megahit/1.1.2 qt/5.4.0 ucsc_tools/2017-05-04
bwa/0.7.12 gdc-client/1.0.1 megan/6.4.4 qt/5.9.1 usearch/5.2.236
bwa/0.7.15 gdc-client/1.3.0 meme/4.11.2 R/3.2.2(default) usearch/6.1.544
bwa/0.7.3a gemini/0.18.0 microbiomeutil/2010-04-29 R/3.2.5 VarDict/1.0
bzip2/1.0.6 gemini/0.20.1 microbiomeutil/r20110519 R/3.3.3 VarDictJava/1.4.9
canu/1.7.1 GEMS-db/1.0 miniconda/3.6 R/3.4.2 VariationHunter_CL/0.04
cdbfasta/0.99 genometools/1.5.8 mothur/1.25.0 R/3.4.4 varscan/2.4.1
cd-hit/4.6.5 gflags/2.2.1 mothur/1.36.1 R/3.5.1 vcf2maf/1.6.6
chimera/1.12 GISTIC/2.0.23 MotionCor2/1.0.5 RAPSearch/2.12 vcftools/0.1.14
circos/0.69.2 git/2.7.1 mpich2/1.4.1p1 RAPSearch/2.23 vep/75
clearcut/1.0.9 glib/2.40.0 MSGFPlus/v10072 rar/5.5.b1 vep/83
cmake/3.7.2 glibc/2.14.1 MSGFPlus/v10089 raxml/7.3.0MPI vep/84
cmake/3.9.3 globus/2.3.5 MSGFPlus/v2017.01.13 raxml/7.3.0OMP ViennaRNA/2.4.9
convading/1.1.6 glog/0.3.5 mummer/4.0.0 raxml/7.3.0Serial vsearch/2.4.1
CovGen/1.0.2 gmap/2017-05-03 MUMmer/3.23 raxml/8.2.8MPI vt/01282016
ctffind/4.0.17 gnuplot/5.2.4 muscle/3.8.31 raxml/8.2.8OMP weblogo/2.8.2
cuda/8.0.61 gromacs/2018.2 mutect/1.1.1 raxml/8.2.8Serial xhmm/1.0
cuda/9.1.85 gromacs/2018.2GPU mutect/1.1.4 RDPTools/2.0.2 xz/5.2.3
cudnn/8.0v5.0 gstreamer/1.12.5 mutect/1.1.7 relion/1.4 zlib/1.2.11
cudnn/8.0v6.0 gtk-doc/1.28 netMHCpan/4.0a relion/2.0.3 zlib/1.2.8
cufflinks/2.2.1 hdf5/1.10.1 novoalign/3.8.02 relion/2.0.3_60
curl/7.56.1 hdf5/1.10.2 oncocator/1.8.0.0 relion/2.1
cutadapt/1.9.1_py2.7.11 hdf5/1.8.20 oncocnv/6.4 relion/3.0b
cutadapt/1.9.1_py2.7.6 hic-dc/1.0 openbabel/2.4.1 rMATS/3.2.5
Bioinfomatics service will be charged at $50 per hands on hour for internal investigators ($60 for external non-profit/academic). Each project is different, so investigators are encouraged to contact us to estimate the necessary hands-on hours for each project. Below are representative analysis services we provide. We provide tutorial/hands-on training as well by the same $50/hr fee-for-service basis.