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
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 192 TB lustre FS 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 edwards.sdsu.edu 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 bioperl biopython bowtie2 cdhit crass diamond fastQC
focus
FOCUS
FragGeneScan
genemark
groopm
idba_ud
jellyfish
last
masurca
mauve
metabat
metagenemark
mira
MUMmer
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 Statistics Deconseq
Annotation
FOCUS
Real time metagenomics
mg-rast
Super FOCUS
Statistics
STAMP
Population genomes
crAss
metabat
ContigClustering

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