Up to date software list with additional information (version etc.) is onlineĦ GBS-related software used during the workshop is pre-installed on BioHPC machines. Windows: NextGENe (SoftGenetics), NGen (DNAStar), GenomeStudio (SoftGenetics). Dell Precision PWS T5400, Quad Core Intel Xeon E GHz CPU, HDD SATA controller with total of 10TB HDD storage, 16GB RAM, NVIDIA Quadro FX570 Graphics Card, 24in LCD monitor.ĥ Software (partial list): Linux: 454 gsassembler, ABySS, ALLPATHS-LG, AMOS, Annovar, ATSAS, Augustus, bamtools, BEDtools, BioPerl, BioPython, Bismark, BLAST, BLAT, Bowtie, Bowtie2, BWA, CBSU RNAseq, CLUSTALW, Cufflinks, exonerate, FASTX, Flexible Adapter Remover, GATK, Genome STRiP, HyPhy, iassembler, IGV, LUCY, LUCY2, MACS, MACS2, MAKER, MAQ, mirdeep2, MMSEQ, MSR-CA Genome Assembler, MUMmer, Netbeans, Novoalign, NovoalignCS, Oases, Picard, Pindel, plink, prinseq, QIIME, R, RepeatMasker, RSEM, Samtools, SOAPdenovo, SOAPdenovo-Trans, SOAPdenovo2, stacks, tabix, Tandem Repeats Finder, TASSEL 3, TASSEL 4, TopHat, trimmomatic, Trinity, vcftools, Velvet, wgs-assembler. Each node is Dell PowerEdge R710 with one quad-core Intel Xeon E5603 CPU, 24GB RAM and 12 disk rack enclosure (4TB disks) connected to LSI e RAID controller configured at RAID6. Two node glusterfs storage cluster with total capacity 80TB. 5 Red Barn Servers with four 16-core AMD Opteron GHz, 13TB HD, 512GB RAM. Red Barn Server with four 12-core AMD Opteron 6172 SKT G34 2.1GHz, 13TB HD, 512GB RAM. Dell PowerEdge R710 with four quad-core Intel Xeon E GHz, 1TB HD, 64GB RAM. Dell Precision T3500n, Quad Core Intel Xeon W GHz CPU, HDD SATA controller with 2 2TB HDD, 24GB RAM, NVIDIA Quadro NVS 295 Graphics Card, 24in LCD monitor. 3 Linux interactive workstations (large monitors). Dell PowerEdge M600 blade server, two quad-core Intel Xeon E GHz CPUs, 16GB RAM, 1TB HD local storage. 3 BioHPC Laboratory is a computational resource configured and optimized for the needs of computational biology Available to Cornell and external users Charged per hour of usage (free for GBS workshop exercises) For details and fee structure, visitĤ Hardware/OS: 31 Linux remote workstations.
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