The data deluge driven by Next Generation Sequencing is transforming life sciences and its computational needs Simon Rasmussen Assistant Professor Center for Biological Sequence Analysis Department of Systems Biology Technical University of Denmark [email protected] Helicobacter acinonychis str Sheeba Helicobacter pylori P12 Helicobacter pylori B8 Helicobacter pylori 26695 Helicobacter pylori G27 Helicobacter pylori B38 Helicobacter pylori HPAG1 Helicobacter pylori Shi470 Helicobacter pylori J99 Helicobacter cinaedi CCUG 18818 Helicobacter hepaticus ATCC 51449 Helicobacter mustelae 12198 Helicobacter bilis ATCC 43879 Helicobacter pullorum MIT 98−5489 Helicobacter canadensis MIT 98−5491 Helicobacter winghamensis ATCC BAA−430 Wolinella succinogenes DSM 1740 Campylobacter concisus 13826 Campylobacter curvus 52592 Campylobacter rectus RM3267 Campylobacter showae RM3277 Campylobacter fetus subsp fetus 82−40 Campylobacter hominis ATCC BAA−381 Campylobacter gracilis RM3268 Sulfurospirillum deleyianum DSM 6946 Nitratiruptor sp SB155−2 Sulfurimonas denitrificans DSM 1251 Arcobacter nitrofigilis DSM 7299 Arcobacter butzleri RM4018 Sulfurovum sp NBC37−1 Nautilia profundicola AmH GU649V1.CD18.3 GU649V1.CD35.0 Fusobacterium sp D11 Fusobacterium sp 3 1 33 Fusobacterium sp 7 1 Fusobacterium nucleatum subsp nucleatum ATCC 25586 Fusobacterium nucleatum subsp nucleatum ATCC 23726 Fusobacterium sp 3 1 27 Fusobacterium sp 4 1 13 Fusobacterium sp 3 1 36A2 Fusobacterium sp 2 1 31 Fusobacterium sp 1 1 41FAA Fusobacterium periodonticum ATCC 33693 Fusobacterium sp D12 Fusobacterium gonidiaformans ATCC 25563 Fusobacterium sp 3 1 5R Fusobacterium varium ATCC 27725 Fusobacterium ulcerans ATCC 49185 Fusobacterium mortiferum ATCC 9817 Sebaldella termitidis ATCC 33386 Leptotrichia goodfellowii F0264 Leptotrichia hofstadii F0254 Leptotrichia buccalis C−1013−b Streptobacillus moniliformis DSM 12112 Nostoc punctiforme PCC 73102 Nostoc sp PCC 7120 Anabaena variabilis ATCC 29413 Nostoc azollae 0708 Trichodesmium erythraeum IMS101 Cyanothece sp PCC 7425 Thermosynechococcus elongatus BP−1 Acaryochloris marina MBIC11017 Synechococcus elongatus PCC 7942 Synechococcus elongatus PCC 6301 Synechocystis sp PCC 6803 Cyanothece sp PCC 8802 Cyanothece sp PCC 8801 Cyanothece sp ATCC 51142 Cyanothece sp PCC 7424 Microcystis aeruginosa NIES−843 Synechococcus sp PCC 7002 cyanobacterium UCYN−A Synechococcus sp WH 8102 Synechococcus sp CC9605 Synechococcus sp CC9902 Synechococcus sp WH 7803 Synechococcus sp CC9311 Prochlorococcus marinus str MIT 9303 Prochlorococcus marinus str MIT 9313 Prochlorococcus marinus str MIT 9211 Prochlorococcus marinus subsp marinus str CCMP1375 Prochlorococcus marinus str NATL2A Prochlorococcus marinus str NATL1A Synechococcus sp RCC307 Prochlorococcus marinus str MIT 9312 Prochlorococcus marinus str MIT 9215 Prochlorococcus marinus str AS9601 Prochlorococcus marinus str MIT 9301 Prochlorococcus marinus str MIT 9515 Prochlorococcus marinus subsp pastoris str CCMP1986 Synechococcus sp JA−3−3Ab Synechococcus sp JA−2−3Ba(2−13) Gloeobacter violaceus PCC 7421 GU729MH0021 GU967MH0067 GU768V1.CD19.0 GU715MH0183 GU439MH0043 GU484V1.UC40.0 GU815MH0137 GU815O2.UC44.0 GU815O2.UC44.2 GU196MH0038 GU306V1.CD28.0 Rothia mucilaginosa DY−18 Rothia mucilaginosa ATCC 25296 Rothia dentocariosa ATCC 17931 Kocuria rhizophila DC2201 Arthrobacter sp FB24 Arthrobacter chlorophenolicus A6 Arthrobacter aurescens TC1 Renibacterium salmoninarum ATCC 33209 Micrococcus luteus NCTC 2665 Micrococcus luteus SK58 Brevibacterium mcbrellneri ATCC 49030 Kytococcus sedentarius DSM 20547 Clavibacter michiganensis subsp sepedonicus Clavibacter michiganensis subsp michiganensis NCPPB 382 Leifsonia xyli subsp xyli str CTCB07 Kineococcus radiotolerans SRS30216 Mobiluncus mulieris 28−1 Mobiluncus mulieris ATCC 35243 Mobiluncus curtisii ATCC 43063 Actinomyces odontolyticus ATCC 17982 Actinomyces odontolyticus F0309 Actinomyces coleocanis DSM 15436 Actinomyces urogenitalis DSM 15434 Actinomyces sp oral taxon 848 str F0332 Arcanobacterium haemolyticum DSM 20595 Cellulomonas flavigena DSM 20109 Sanguibacter keddieii DSM 10542 Xylanimonas cellulosilytica DSM 15894 Jonesia denitrificans DSM 20603 Beutenbergia cavernae DSM 12333 Brachybacterium faecium DSM 4810 Frankia sp EAN1pec Frankia alni ACN14a Frankia sp CcI3 Geodermatophilus obscurus DSM 43160 Kribbella flavida DSM 17836 Nocardioides sp JS614 Aeromicrobium marinum DSM 15272 Propionibacterium freudenreichii subsp shermanii CIRM−BIA1 Propionibacterium acnes J139 Propionibacterium acnes J165 Propionibacterium acnes KPA171202 Propionibacterium acnes SK187 Propionibacterium acnes SK137 Bifidobacterium bifidum NCIMB 41171 GU234V1.CD36.0 Bifidobacterium longum subsp infantis ATCC 15697 Bifidobacterium longum subsp longum ATCC 55813 Bifidobacterium longum subsp infantis CCUG 52486 Bifidobacterium longum subsp longum F8 Bifidobacterium longum DJO10A Bifidobacterium longum NCC2705 Bifidobacterium longum subsp longum JDM301 Bifidobacterium breve DSM 20213 GU69V1.CD36.0 Bifidobacterium adolescentis ATCC 15703 Bifidobacterium adolescentis L2−32 Bifidobacterium pseudocatenulatum DSM 20438 Bifidobacterium catenulatum DSM 16992 Bifidobacterium dentium Bd1 Bifidobacterium dentium ATCC 27678 Bifidobacterium angulatum DSM 20098 Bifidobacterium animalis subsp lactis AD011 Bifidobacterium animalis subsp lactis DSM 10140 Bifidobacterium animalis subsp lactis Bl−04 Bifidobacterium gallicum DSM 20093 Gardnerella vaginalis ATCC 14019 Gardnerella vaginalis 409−05 Parascardovia denticolens F0305 Scardovia inopinata F0304 Tropheryma whipplei str Twist Tropheryma whipplei TW0827 Tsukamurella paurometabola DSM 20162 Rhodococcus jostii RHA1 Rhodococcus opacus B4 Rhodococcus erythropolis PR4 Rhodococcus erythropolis SK121 Rhodococcus equi ATCC 33707 Nocardia farcinica IFM 10152 Gordonia bronchialis DSM 43247 Mycobacterium abscessus ATCC 19977 Mycobacterium sp JLS Mycobacterium sp KMS Mycobacterium sp MCS Mycobacterium smegmatis str MC2 155 Mycobacterium gilvum PYR−GCK Mycobacterium vanbaalenii PYR−1 Mycobacterium tuberculosis F11 Mycobacterium tuberculosis KZN 1435 Mycobacterium tuberculosis H37Rv Mycobacterium tuberculosis CDC1551 Mycobacterium tuberculosis H37Ra Mycobacterium bovis BCG str Tokyo 172 Mycobacterium bovis BCG str Pasteur 1173P2 Mycobacterium bovis AF212297 Mycobacterium marinum M Mycobacterium ulcerans Agy99 Mycobacterium parascrofulaceum ATCC BAA−614 Mycobacterium avium subsp paratuberculosis K−10 Mycobacterium avium 104 Mycobacterium leprae TN Nakamurella multipartita DSM 44233 Actinosynnema mirum DSM 43827 Saccharopolyspora erythraea NRRL 2338 Saccharomonospora viridis DSM 43017 ostearicum SK141 Corynebacterium pseudogenitalium ATCC 33035 Bacteroides ovatus SD CC 2a Bacteroides xylanisolvens SD CC 1b Bacteroides sp D1 Bacteroides sp 2 1 22 Bacteroides xylanisolvens XB1A Bacteroides ovatus SD CMC 3f Bacteroides ovatus ATCC 8483 Bacteroides sp 2 2 4 Bacteroides sp D2 Bacteroides caccae ATCC 43185 Bacteroides finegoldii DSM 17565 Bacteroides thetaiotaomicron VPI−5482 Bacteroides sp 1 1 6 Bacteroides fragilis NCTC 9343 Bacteroides fragilis YCH46 Bacteroides sp 2 1 16 Bacteroides sp 3 2 5 Bacteroides fragilis 3 1 12 Bacteroides cellulosilyticus DSM 14838 Bacteroides intestinalis DSM 17393 Bacteroides sp D20 Bacteroides uniformis ATCC 8492 Bacteroides eggerthii DSM 20697 Bacteroides stercoris ATCC 43183 GU633MH0143 Bacteroides vulgatus PC510 Bacteroides sp 4 3 47FAA Bacteroides vulgatus ATCC 8482 Bacteroides dorei DSM 17855 Bacteroides sp 3 1 33FAA Bacteroides dorei 5 1 36D4 Bacteroides sp 9 1 42FAA Bacteroides coprocola DSM 17136 Bacteroides coprophilus DSM 18228 Bacteroides plebeius DSM 17135 GU702MH0047 GU702MH0135 GU462V1.CD38.0 GU116MH0047 GU116MH0006 GU755V1.CD19.0 GU617MH0046 GU5226O2.UC43.0 GU891MH0057 Prevotella tannerae ATCC 51259 GU474MH0006 Prevotella bergensis DSM 17361 GU924MH0069 Prevotella bivia JCVIHMP010 Prevotella melaninogenica ATCC 25845 Prevotella melaninogenica D18 Prevotella veroralis F0319 GU164V1.UC56.0 Prevotella copri DSM 18205 Prevotella buccae D17 Prevotella oris F0302 GU1320MH0057 GU1320O2.UC57.0 GU301V1.CD13.0 Prevotella buccalis ATCC 35310 Prevotella timonensis CRIS 5C−B1 Prevotella sp oral taxon 472 str F0295 Prevotella sp oral taxon 317 str F0108 Prevotella sp oral taxon 299 str F0039 GU255MH0011 GU255V1.UC55.4 GU1185MH0107 GU1058V1.CD19.0 GU592MH0168 GU520MH0045 GU520MH0012 Prevotella ruminicola 23 GU20MH0012 GU20MH0061 GU51O2.UC37.0 GU118V1.CD15.3 Parabacteroides merdae ATCC 43184 Parabacteroides johnsonii DSM 18315 Bacteroides sp 2 1 7 Bacteroides sp 2 1 33B Parabacteroides sp D13 Parabacteroides distasonis ATCC 8503 GU2MH0020 GU2MH0074 GU279MH0020 GU279O2.UC18.2 Porphyromonas uenonis 60−3 Porphyromonas endodontalis ATCC 35406 Porphyromonas gingivalis ATCC 33277 Porphyromonas gingivalis W83 GU1031V1.CD20.4 GU927V1.CD29.0 GU927O2.UC40.2 GU927O2.UC40.0 GU873O2.UC60.0 GU485O2.UC60.0 Candidatus Azobacteroides pseudotrichonymphae genomovar CFP2 GU67O2.UC48.2 GU67MH0012 Alistipes putredinis DSM 17216 GU29MH0002 GU29MH0074 Alistipes shahii WAL 8301 GU268MH0054 GU157V1.UC11.5 GU14MH0012 GU14O2.UC48.2 GU788MH0016 GU788V1.UC49.1 GU561O2.UC51.2 GU561V1.UC49.1 GU709MH0158 GU770MH0006 GU770MH0022 GU545MH0009 GU435MH0012 GU514MH0009 GU514MH0031 GU1060MH0044 GU831MH0143 GU831MH0071 Pedobacter heparinus DSM 2366 Sphingobacterium spiritivorum ATCC 33300 Sphingobacterium spiritivorum ATCC 33861 Cytophaga hutchinsonii ATCC 33406 Dyadobacter fermentans DSM 18053 Spirosoma linguale DSM 74 Flavobacterium psychrophilum JIP0286 Flavobacterium johnsoniae UW101 Croceibacter atlanticus HTCC2559 Gramella forsetii KT0803 Zunongwangia profunda SM−A87 Robiginitalea biformata HTCC2501 Capnocytophaga ochracea DSM 7271 Capnocytophaga sputigena ATCC 33612 Capnocytophaga gingivalis ATCC 33624 Flavobacteriaceae bacterium 3519−10 Chryseobacterium gleum ATCC 35910 Chitinophaga pinensis DSM 2588 Candidatus Amoebophilus asiaticus 5a2 Blattabacterium sp (Periplaneta americana) str BPLAN Blattabacterium sp (Blattella germanica) str Bge Candidatus Carsonella ruddii PV Ruminococcus gnavus ATCC 29149 Candidatus Sulcia muelleri GWSS Candidatus Sulcia muelleri DMIN Candidatus Sulcia muelleri SMDSEM Salinibacter ruber Salinibacter ruber DSM 13855 Rhodothermus marinus DSM 4252 Chlorobium luteolum DSM 273 Chlorobium phaeovibrioides DSM 265 Pelodictyon phaeoclathratiforme BU−1 Chlorobium limicola DSM 245 Chlorobium phaeobacteroides DSM 266 Chlorobium chlorochromatii CaD3 Chlorobaculum parvum NCIB 8327 Chlorobium tepidum TLS Prosthecochloris aestuarii DSM 271 Chlorobium phaeobacteroides BS1 Chloroherpeton thalassium ATCC 35110 Gemmatimonas aurantiaca T−27 Fibrobacter succinogenes subsp succinogenes S85 Chlamydia trachomatis AHAR−13 Chlamydia trachomatis BTZ1A828OT Chlamydia trachomatis DUW−3CX Chlamydia trachomatis BJali20OT Chlamydia trachomatis L2bUCH−1proctitis Chlamydia trachomatis 434Bu Chlamydia muridarum Nigg Chlamydophila pneumoniae J138 Chlamydophila pneumoniae TW−183 Chlamydophila pneumoniae CWL029 Chlamydophila pneumoniae AR39 Chlamydophila felis FeC−56 Chlamydophila caviae GPIC Chlamydophila abortus S263 Candidatus Protochlamydia amoebophila UWE25 Waddlia chondrophila WSU 86−1044 GU154MH0012 GU154MH0002 GU154V1.CD31.0 GU344V1.CD7.4 Akkermansia muciniphila ATCC BAA−835 Methylacidiphilum infernorum V4 Opitutus terrae PB90−1 Coraliomargarita akajimensis DSM 45221 Rhodopirellula baltica SH 1 Pirellula staleyi DSM 6068 Planctomyces limnophilus DSM 3776 Borrelia burgdorferi B31 Borrelia burgdorferi ZS7 Borrelia afzelii PKo Borrelia garinii PBi Borrelia turicatae 91E135 Borrelia hermsii DAH Borrelia recurrentis A1 Borrelia duttonii Ly Treponema vincentii ATCC 35580 Treponema denticola ATCC 35405 Treponema pallidum subsp pallidum SS14 Treponema pallidum subsp pallidum str Nichols Leptospira biflexa serovar Patoc strain Patoc 1 (Ames) Leptospira biflexa serovar Patoc strain Patoc 1 (Paris) Leptospira borgpetersenii serovar Hardjo−bovis L550 Leptospira borgpetersenii serovar Hardjo−bovis JB197 Leptospira interrogans serovar Copenhageni str Fiocruz L1−130 Leptospira interrogans serovar Lai str 56601 Brachyspira hyodysenteriae WA1 Brachyspira murdochii DSM 12563 Elusimicrobium minutum Pei191 uncultured Termite group 1 bacterium phylotype Rs−D17 Thermosipho melanesiensis BI429 Thermosipho africanus TCF52B Fervidobacterium nodosum Rt17−B1 Thermotoga petrophila RKU−1 Thermotoga naphthophila RKU−10 Thermotoga sp RQ2 Thermotoga maritima MSB8 Thermotoga neapolitana DSM 4359 Thermotoga lettingae TMO Kosmotoga olearia TBF 1951 Petrotoga mobilis SJ95 Dictyoglomus turgidum DSM 6724 Dictyoglomus thermophilum H−6−12 Coprothermobacter proteolyticus DSM 5265 Candidatus Cloacamonas acidaminovorans Dehalococcoides ethenogenes 195 Dehalococcoides sp VS Dehalococcoides sp GT Dehalococcoides sp CBDB1 Dehalococcoides sp BAV1 Dehalogenimonas lykanthroporepellens BL−DC−9 Sphaerobacter thermophilus DSM 20745 Thermomicrobium roseum DSM 5159 Thermobaculum terrenum ATCC BAA−798 Chloroflexus sp Y−400−fl Chloroflexus aurantiacus J−10−fl Chloroflexus aggregans DSM 9485 Roseiflexus castenholzii DSM 13941 Roseiflexus sp RS−1 Herpetosiphon aurantiacus DSM 785 Synergistetes bacterium SGP1 Aminobacterium colombiense DSM 12261 Anaerobaculum hydrogeniformans ATCC BAA−1850 Thermanaerovibrio acidaminovorans DSM 6589 Pyramidobacter piscolens W5455 Jonquetella anthropi E3 33 E1 Meiothermus ruber DSM 1279 Meiothermus silvanus DSM 9946 Thermus thermophilus HB8 Thermus thermophilus HB27 Deinococcus deserti VCD115 Deinococcus geothermalis DSM 11300 Deinococcus radiodurans R1 Truepera radiovictrix DSM 17093