SLIDE 1
Bioinformatics Outline
- What is bioinformatics?
– Who are bioinformaticians?
- Hardware
- Software
What is bioinformatics?
Bioinformatics Outline What is bioinformatics? Who are - - PowerPoint PPT Presentation
Bioinformatics Outline What is bioinformatics? Who are - - PowerPoint PPT Presentation
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 Someone to help me between experiments
SLIDE 2
SLIDE 3
What is bioinformatics?
Someone to analyze my data Someone to help me think about my data A p e r s
- n
w h
- w
r i t e s c
- m
p l e x a l g
- r
i t h m s A p e r s
- n
w h
- k
n
- w
s w h a t a n H M M i s That bloke who fixes my computer Someone who builds websites People sitting in a dark room analyzing data The boring stuff I do between experiments perl python R linux java C++ bash ruby HTML
SLIDE 4
Who are bioinformaticians?
- Scientists trying to get tenure, get grants,
publish papers, train students
- Scientists trying to help others analyze their
data
SLIDE 5
Who are bioinformaticians?
YOU!
SLIDE 6
Hardware
SLIDE 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 – fjle access available via SSH or
web service
$12,500
SLIDE 8
Computers
- My cluster
– 51 node cluster – most nodes: 16 cpus, 8 cores each,132 GB RAM, 1TB
local storage (/usr/data), infjniband interconnects
– (6,528 cores; 6,732 GB RAM; 50 TB scratch storage)
- 192 TB lustre FS
– connected to most nodes via infjniband
SLIDE 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
SLIDE 10
Computers
- fjle servers and back up servers
– 4 secret servers! – 48TB backups and archival storage
SLIDE 11
Software
SLIDE 12
Software
- Locally installed software
- Remote (web) software
SLIDE 13
Local Software
- groopm
- idba_ud
- jellyfjsh
- jellyfjsh
- 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
- scafgold_builder
- seed-servers
- spades
- tagcleaner
- tRNAscan-SE
- velvet
SLIDE 14
Metagenomics Processing
B i n n i n g r e a d s Contamination removal C
- n
t i g C l u s t e r i n g F u n c t i
- n
a l A s s i g n m e n t s G e n e P r e d i c t i
- n
M e r g e p a i r e d
- e
n d r e a d s P r e p r
- c
e s s i n g Taxonomic assignments
SLIDE 15
Metagenomics
- Quality control –
Prinseq
- Deconseq
- Annotation
– FOCUS – Real time
metagenomics
– mg-rast – Super FOCUS
- Statistics
– STAMP
- Population genomes
– crAss – metabat – ContigClustering
SLIDE 16
Metagenomics Processing
AbundanceBin CompostBin concoct crAss tetra Contig clustering FragGeneScan GlimmerMG MetaGeneAnnotator MetaGeneMark MetaGun Orphelia Prodigal Gene Prediction FASTQC FastX Toolkit fjtGCP NGS QC Toolkit Non-pareil Prinseq QC-Chain Streaming Trim Preprocessing 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