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Bioinformatics Outline

Bioinformatics Outline. What is bioinformatics? Who are bioinformaticians? Hardware Software. What is bioinformatics?. What is bioinformatics?. Someone to analyze my data. The boring stuff I do between experiments. Someone to help me think about my data.

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Bioinformatics Outline

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  1. Bioinformatics Outline What is bioinformatics? Who are bioinformaticians? Hardware Software

  2. What is bioinformatics?

  3. What is bioinformatics? Someone to analyze my data The boring stuff I do between experiments Someone to help me think about my data People sitting in a dark room analyzing data A person who writes complex algorithms perl python R linux java C++ bash ruby HTML A person who knows what an HMM is That bloke who fixes my computer Someone who builds websites

  4. Who are bioinformaticians? Scientists trying to get tenure, get grants, publish papers, train students Scientists trying to help others analyze their data

  5. Who are bioinformaticians? YOU!

  6. Hardware

  7. Torrent Server Recommended Torrent Server Processors - Two Six-core processors RAM - 48 GB RAM HDD Capacity - Eight 2 TB Hard drives in RAID 5 with 12 TB usable Network – Quad port gigabit NIC GPU - NVIDIA Graphic Processor Unit Chassis – Dell Precision T7500 tower. No rack mount available. Monitor⁄Keyboard – not included – file access available via SSH or web service $12,500

  8. Computers My cluster 51 node cluster most nodes: 16 cpus, 8 cores each,132 GB RAM, 1TB local storage (/usr/data), infiniband interconnects (6,528 cores; 6,732 GB RAM; 50 TB scratch storage) 192 TB lustre FS connected to most nodes via infiniband

  9. Computers rambox 24 processors with 6 cores each 198 MB RAM edwards.sdsu.edu lab web server 24 processors, 6 cores each 50M RAM 19TB RAID 6 storage 18TB USED

  10. Computers file servers and back up servers 4 secret servers! 48TB backups and archival storage

  11. Software

  12. Software Locally installed software Remote (web) software

  13. Local Software groopm idba_ud jellyfish jellyfish last masurca mauve metabat metagenemark mira MUMmer bioperl biopython bowtie2 cdhit crass diamond fastQC focus FOCUS FragGeneScan genemark • Muscle • PEAR • phylip • prinseq • qiime • qudaich • rapsearch • scaffold_builder • seed-servers • spades • tagcleaner • tRNAscan-SE • velvet

  14. Metagenomics Processing Merge paired-end reads Preprocessing Functional Assignments Taxonomic assignments Contamination removal Gene Prediction Contig Clustering Binning reads

  15. Metagenomics Quality control – Prinseq Deconseq Annotation FOCUS Real time metagenomics mg-rast Super FOCUS Statistics STAMP Population genomes crAss metabat ContigClustering

  16. Metagenomics Processing Contig clustering Preprocessing Gene Prediction FragGeneScan GlimmerMG MetaGeneAnnotator MetaGeneMark MetaGun Orphelia Prodigal FASTQC FastX Toolkit fitGCP NGS QC Toolkit Non-pareil Prinseq QC-Chain Streaming Trim AbundanceBin CompostBin concoct crAss tetra Taxonomic assignment Functional assignment CLAMS Sequedex DiScRIBinATE SORT-ITEMS genometa SPANNER GSMer SPHINX PPLACER TaxSOM RTMg Treephyler CARMA myTaxa FOCUS PhylopythiaS KRAKEN phymmbl LMAT RAIphy MEGAN TACOA Metaplan Taxy

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