Bioinformatics at IITA

www.iita.orgA member of CGIAR consortium
Bioinformatics @ IITA
Andreas Gisel
IITA – Bioscience & Bioinformatics

 Bioinformatics – definition and introduction
 Bioinformatics @ IITA
 Bioinformatics & IITA

Bioinformatics - definition
Bio – Biology, Life Sciences
Informatics – computational sciences
DATA INTERPRETATIONS
RESULTS
Bio informatics

RESULTS
Data Repositories
Knowledge

Bioinformatics is an interdisciplinary science that develops and
improves on methods of analyzing biological data and storing,
retrieving, organizing, and visualizing them.
This is in order to support to solve biological problems and
discover the wealth of biological information hidden in biological
data.

?
Biological Data
Descriptions
Pictures

Descriptions
Pictures
Sequences
Biological Data

Descriptions
Pictures
Sequences
 Protein
 RNA
 DNA
 First fully sequenced bio-sequence
 amino acid of insulin (51aa) 1955
 First fully sequence nucleic acid
 tRNA (75nt) 1965
 First DNA
 Bacteriophage (5375nt) 1977
 DNA sequencing
 Sanger sequencing technology (1975)
 Pyrosequencing (Next Generation sequencing 2004)
 First fully sequenced bio-sequence
 amino acid of insulin (51aa) 1955
 First fully sequence nucleic acid
 tRNA (75nt) 1965
 First DNA
 Bacteriophage (5375nt) 1977
 DNA sequencing
 Sanger sequencing technology (1975)
 Pyrosequencing (Next Generation sequencing 2004)
Biological Data

Descriptions
Pictures
Sequences
 Protein
 RNA
 DNA
Structures
Biological Data

Descriptions
Pictures
Sequences
 Protein
 RNA
 DNA
Structures
 Protein
 RNA
Biological Data

Descriptions
Pictures
Sequences
 Protein
 RNA
 DNA
Structures
 Protein
 RNA
Interactions
Biological Data

Descriptions
Pictures
Sequences
 Protein
 RNA
 DNA
Structures
 Protein
 RNA
Interactions
Expressions
Biological Data

Up to 600’000’000’000
(600GB) bases per
experiment
Data Explosion
Descriptions
Pictures
Sequences
 Protein
 RNA
 DNA
Structures
 Protein
 RNA
Interactions
Expressions
Microarray
High Throughput sequencing
Up to 1 million data points
per experiment
NGS
(Next Generation Sequencing)

Descriptions
Pictures
Sequences
 Protein
 RNA
 DNA
Structures
 Protein
 RNA
Interactions
Expressions
Data Explosion

Data Analysis – DNA/RNA sequences
Sequence without
knowledge connected to it
is meaningless!
What to do?
Sequence similarity
Finding genes and regulatory
elements
Functional analysis of genes
Homology
Polymorphism
BIO
INFO
RM
ATICS

Data Analysis
So we need bioinformatics tools and reference data
Hardware – Computing infrastructure (CPU, RAM, Storage)
Tools – Programs that process your data
Reference data – Databases for existing data
INTERNET– connection to external Databases

Personel
Livia Stavolone – molecular biologist
Deborah Adeyele – student (training in bioinformatics and non-coding RNA)
Toyin Abdulsalam – research fellow (bioinformatics and transcriptom analysis)
Andreas Gisel
Whole Bioscience Team

Hardware – Computing infrastructure (CPU, RAM, Storage)
HP Blade, with:
3 blades with each 2 16-core processors (AMD
Opteron Processor 6272),
384Gb RAM
2Tb attached storage (DAS)
8TB attached storage (NAS)
The operating system is Ubuntu 14.04.1 LTS
installed via biolinux 8.

Basic bioinformatics services mainly based on sequence analysis
Next Generation Sequencing data analysis pipelines including:
GBS (genotyping by sequencing) data analysis and SNP calling
Transcriptomics (RNA-seq) mapping, assembly and expression profiling
smallRNA data analysis: discovery and expression profiling
DNA methylation (BS-seq) data analysis
DNA (shotgun) assembly and variation calling
Genome annotation using different data pipelines and visualization
Customized approaches using perl and shell scripting

GBS (genotyping by sequencing) data analysis and SNP calling
Cassava
1200GB compressed sequence data (~5500 accessions) SNP matrix
5500 x ~160’000SNPs
Yam
200GB compressed sequence data (~800 accessions) 800 x ~25’000SNPs
Raw sequencing data SNP matrix
Cornell SNP calling
(TASSEL)
Broad SNP calling (GATK)

Ismail Rabbi
SNP matrix
Cornell

SNP matrix
In-house

SNP matrix
Histogram of IBS.num
Distance (1 PSA)−
Frequency
0.00 0.05 0.10 0.15 0.20 0.25
01000200030004000

SNP matrix
0123
TDr_2859:250398193
TDr_2034:250398313
TDr_3469:250398200
TDr_3373:250398243
TDr_2110:250398311
TDr_2161:250405306
TDr_3681:250446471
TDr_1723:250405313
TDr_2504:250398071
TDr_3783:250398348
TDr_2681:250398257
TDr_2693:250398258
TDr_3414:250398323
TDr_3446:250398325
TDr_2558:250398064
TDr_2975:250398255
TDr_1839:250405314
TDr_2071:250405299
TDr_2745:250398197
TDr_3288:250398195
TDr_3291:250398250
TDr_2561:250398237
TDr_2973:250398202
TDr_1807:250378524
TDr_2355:250398082
TDr_3680:250398349
Tdr_08_5_1__T_:250405386
TDr_2554:250398059
TDr_3801:250378567
TDr_2330:250405365
TDr_1631:250446476
TDr_2645:250446466
TDr_3721:250446461
TDr_2471:250398486
TDr_2664:250398502
Tdr_08_5_2:250446274
TDr_2777__T_:250446212
TDr_3134:250446387
TDr_3564__M_:250446214
TDr_2377:250446347
TDr_3519:250446472
TDr_2660:250398507
TDr_3592:250398498
TDr_3678:250398437
TDr_1940:250378509
TDr_1598:250398530
TDr_2372:250398115
TDr_1958:250398261
TDr_1615:250378538
TDr_2084:250398094
TDr_1769:250378529
TDr_1724:250378548
TDr_2015:250378514
TDr_3660:250378564
TDr_12_00417:250446390
TDr_2688:250446384
TDr_1925:250398234
Tdr_3956:250398387
TDr_1799:250405308
TDr_2158:250405309
TDr_2007:250398314
TDr_4152:250398227
TDr_2997:250398203
TDr_3389:250398244
TDr_2207:250398236
TDr_2904:250398248
TDr_3590:250446475
TDr_2480:250398272
TDr_2257:250398269
TDr_3466:250398324
TDr_2577:250398057
TDr_2533:250446339
TDr_1500:250398130
TDr_08_00640:250446344
TDr_2591:250398320
TDr_4020:250398355
TDr_1553:250398125
TDr_2237:250398315
TDr_2555:250398058
TDr_3310:250398253
TDr_1829:250398360
TDr_2623:250398241
TDr_2687:250398184
TDr_4191:250398224
TDr_3856:250398388
TDr_2886:250398182
TDr_2726:250398361
TDr_1577:250398120
TDr_1676:250405312
TDr_2532:250398060
TDr_1576:250405316
TDr_2136:250398089
TDr_2580:250398068
TDr_3501:250398363
TDr_1828:250405307
TDr_2320:250405303
TDr_1799:250398131
Amola:250398136
amola_m22:250398144
Tdr_08_00083:250405362
Tdr_08_00161:250405360
TDr_2365:250398117
Tdr_09_00001:250398376
TDr_2435:250398076
TDr_3419:250378576
TDr_3316:250446374
TDr_2106:250446457
TDr_3536:250378584
TDr_3547:250378577
TDr_2926:250378587
TDr_3461:250378581
TDr_1492:250378499
TDr_1817:250378526
TDr_2998:250378591
TDr_2018:250378507
TDr_3593:250378573
TDr_3002:250378590
TDr_3433:250378559
TDr_3325:250398506
TDr_2683:250446448
TDr_2291__T_:250405370
TDr_3376:250378552
TDr_3585:250378572
TDr_1876:250378519
TDr_2009:250378513
TDr_2726:250446450
TDr_4017:250446446
TDr_3374:250446362
TDr_2643:250398510
TDr_2636:250446379
TDr_3983:250446354
TDr_2903:250446389
TDr_1601:250446464
TDr_1928:250446459
TDr_2167:250446452
TDr_3985:250398521
TDr_2928:250398492
TDr_4005:250398522
TDr_2623:250398488
TDr_3320:250446386
TDr_3887:250446341
TDr_1495:250378501
TDr_1937:250405368
TDr_1688:250378551
TDr_1809:250378525
TDr_2294:250398110
TDr_2441:250398079
TDr_2506:250398276
TDr_1543:250405321
TDr_2287:250398108
TDr_2512:250398065
TDr_2242:250398103
TDr_2273:250398107
TDr_3003__M_:250405387
TDr_1825:250398233
TDr_3961:250398353
TDr_2458:250398265
TDr_2698:250398208
TDr_3508:250398211
TDr_3828:250398389
TDr_4028:250398220
TDr_1932:250398262
TDr_3287:250398205
TDr_3623:250398213
TDr_2171:250398310
TDr_2618:250398317
TDr_2128:250398277
TDr_2749:250398252
TDr_1559:250398124
TDr_2348:250398113
Tdr_09_00023__M_:250446211
TDr_2467:250446348
TDr_4067:250446445
TDr_2670:250398503
TDr_3301:250398499
TDr_2990:250398487
omi_efun:250398451
TDr_2366:250398116
TDr_3368:250378553
TDr_3569:250378580
TDr_1568:250398529
TDr_1756:250378542
TDr_2104:250398087
TDr_2131:250405300
TDr_1760:250378531
TDr_3322:250398185
TDr_1630:250378541
TDr_2094:250398093
TDr_2248:250398104
TDr_3671:250378565
TDr_2770:250398491
TDr_1804:250378530
TDr_2126:250398086
TDr_2581:250398067
TDr_2059:250398092
TDr_1686:250378535
TDr_3610:250398483
TDr_2431:250398075
TDr_2466:250446200
TDr_3288:250446345
TDr_1513:250398126
TDr_2347:250398119
TDr_2149:250405310
TDr_2642:250398063
TDr_2333:250405301
TDr_1858:250405374
TDr_2035:250398097
TDr_2400:250398073
Aloshi_B5B:250378503
TDr_1489:250378502
TDr_2991:250378588
TDr_3010:250378589
TDr_1663:250378545
TDr_3886:250378561
TDr_1977:250446315
TDr_2342:250446365
TDr_1603:250446201
TDr_08_00045:250446343
TDr_4086:250398465
TDr_1711:250378550
TDr_1966:250378511
TDr_1649:250378543
TDr_3383:250378557
TDr_3633:250398519
Tdr_08_01029:250446196
TDr_1764:250378532
TDr_3637:250446360
TDr_2226:250446449
TDr_3333:250398505
TDr_4087:250398466
TDr_2119:250405304
TDr_2692:250398188
TDr_3312:250398187
TDr_2694:250398186
TDr_2432:250398358
TDr_1650:250405315
TDr_1763:250405317
TDr_2229:250398229
TDr_3621:250398214
TDr_2406:250398070
TDr_3002:250398254
TDr_2239:250398102
TDr_2593:250398319
TDr_2210:250398100
TDr_2931:250405375
TDr_2338:250398111
TDr_2363:250398085
TDr_2763:250398489
TDr_3357:250398501
TDr_3682:250398438
TDr_4154:250398470
TDr_1895:250398512
TDr_3620:250398474
TDr_3616:250398482
TDr_2915:250378586
TDr_3551:250378578
TDr_3594:250378574
TDr_1585:250378540
TDr_3452:250378558
TDr_1827:250378528
TDr_3472:250378582
TDr_3965:250378560
TDr_3016:250446380
TDr_2970:250398496
TDr_3507:250398493
TDr_1669:250378533
TDr_1939:250378515
TDr_2197:250398099
TDr_1621:250378537
TDr_3820:250378568
TDr_2669:250446381
TDr_2650:250398509
TDr_3605:250446382
TDr_2022:250378508
TDr_1832:250378516
TDr_4187:250398511
TDr_2225:250405376
TDr_2958:250398198
TDr_1790:250405295
TDr_3863:250378562
TDr_1826:250378527
TDr_2292:250398109
TDr_1881:250446357
TDr_1505:250398527
TDr_3648:250446462
TDr_2611:250398062
TDr_2048:250398090
TDr_3978:250398520
TDr_3400:250378556
TDr_2564:250446375
TDr_3408:250378555
TDr_1828:250378522
TDr_1717:250378549
TDr_1956:250378512
TDr_2965:250398495
TDr_4038:250446458
TDr_2678:250398504
TDr_2936:250398484
TDr_2946:250446349
TDr_2456:250446350
TDr_2710:250446469
TDr_2897:250398183
TDr_1622:250405318
TDr_2262:250398106
TDr_2401:250398072
TDr_2530:250398316
TDr_2754:250398196
TDr_3338:250398245
TDr_2295:250405305
Pouna__T_:250446267
TDr_2155:250446473
TDr_3473:250378583
TDr_1628:250378536
TDr_2121:250446453
TDr_3371:250398517
TDr_1922:250446385
TDr_2078:250398095
Donte:250398461
TDr_2343:250398118
TDr_2032:250446316
TDr_1684:250378534
TDr_1509:250398528
TDr_1907:250378521
Tdr_08_00861:250446205
TDr_12_00506:250446397
TDr_2350:250398084
TDr_3663:250446463
TDr_1761:250446388
TDr_Adaka_m4:250378497
TDr_3584:250378571
Aluma_411:250398145
TDr_idu_ekpeye:250405319
TDr_1562:250398122
TDr_2323:250405302
TDr_2017:250378506
TDr_2201:250446465
Pepa_B7:250398138
TDr_2211:250398101
Chk_TDr_89_02677:250398114
TDr_1667:250398531
TDr_3544:250398494
TDr_1818:250398518
TDr_2159:250446217
TDr_Obangu_B2H1:250378498
TDr_4155:250398514
TDr_4168:250398515
TDr_1610:250378539
TDr_3825:250378569
Obioturugu_H6:250398135
Tdr_96_02433:250398444
Ehobia:250398441
Tdr_05_00466:250398443
TDr_2033:250446283
TDr_4033:250446376
TDr_2782:250398481
TDr_2701:250446451
TDr_2724:250398513
TDr_2948:250398485
TDr_3852:250378570
TDr_3296:250398490
TDr_3567:250378579
TDr_3766:250378566
TDr_3882:250378563
TDr_1569:250398121
TDr_2266:250398266
TDr_3447:250398199
TDr_2175:250398309
TDr_2297:250405371
TDr_2439:250398077
TDr_2484:250398081
Tdr_08_01229:250446278
Tdr_08_01228:250446277
TDr_12_00476:250446398
TDr_12_00506:250446393
TDr_08_00164:250446358
TDr_12_00446:250446392
Tdr_08_00001:250446225
Tdr_08_00091:250446223
08_00105:250446336
TDr_3649:250446361
Tdr_11_00787:250446252
Tdr_08_00104:250446234
Tdr_08_00027:250446269
Tdr_08_00013:250446226
Tdr_08_00268:250446258
Tdr_08_00008:250446204
Tdr_08_00185:250446232
Tdr_09_00055__T_:250446218
TDr__608:250446254
Tdr_08_00132:250446359
Tdr_08_00146__M_:250446222
Tdr_08_00744:250446251
Tdr_08_01932:250446280
Tdr_95_01932:250446189
Tdr_08_00132:250446248
Tdr_09_00050:250446241
Tdr_08_00055:250446270
09_00267:250446321
Tdr_08_00149__M_:250446233
TDr_08_00197:250446364
09_00216:250446324
Tdr_09_00125:250446271
09_00070:250446331
09_00091:250446330
09_00189:250446322
TDr_13_00330:250446488
Tdr_09_00644:250446282
Tdr_09_00220__T_:250446199
Tdr_97_00777:250446247
TDr_09_00131:250446368
Tdr_89_02672:250446236
Tdr_09_00054:250446209
09_00049:250446328
09_01932:250446319
Tdr_09_00374:250446195
09_00226:250446332
Tdr_08_00090__M_:250446237
TDr_09_00018:250446366
Tdr_09_00107:250446273
09_00029:250446337
TDr_13_00350:250446489
TDr__13_00366:250446505
09_00064:250446327
09_00124:250446326
TDr_97_00917:250446353
Tdr_08_00794:250446227
TDr_13_00273:250446485
TDr__13_00444:250446479
Tdr_05_00046:250398440
Tdr_01_00037:250398469
Tdr_09_00240:250446240
TDr__12_00152:250446515
Tdr_08_00140:250446231
Tdr_08_00758__M_:250446230
TDr05_00807:250446378
TDr_97_00793:250446352
Ehuru__M_:250446192
Tdr_08_00620:250446224
TDr_08_00617:250446356
Tdr_08_00207:250446216
TDr_08_21_3:250446363
Tdr_08_00140:250446263
Tdr_08_00799:250446262
Tdr_08_00651:250446191
Tdr_08_00648:250446238
Tdr_08_00747:250446210
Tdr08_00707__T_:250446276
TDr__13_00285:250446499
96_01724:250446333
TDr_1608:250446470
TDr_3510:250446447
TDr_3785:250398479
TDr_2655:250398508
Tdr_97_00583:250398453
TDr_2663:250446194
Tdr_11_00799:250446272
TDr__13_00354:250446506
TDr__13_00452:250446492
Tdr_05_00389__M_:250446207
TDr_08_01164:250446338
TDr_93_2:250446370
TDr__12_00417:250446536
TDr__13_00125:250446491
TDr__13_00050:250446486
TDr__13_00061:250446496
TDr__13_00431:250446501
Tdr_11_00787:250398449
Tdr_05_00356:250398462
Tdr_05_00530:250398473
TDr_12_00465:250446401
Tdr_05_00303:250446261
Tdr_05_00432:250398439
Tdr_95_18544:250398459
TDr_2514:250446342
Tdr_03_00180:250398457
Tdr_05_00632:250398463
Tdr_05_00694:250398458
TDr_4180:250398472
TDr_3824:250398436
TDr_1536:250446371
TDr_12_00422:250446443
TDr__12_00439:250446510
TDr__12_00178:250446525
TDr__12_00254:250446537
TDr__12_00425:250446518
TDr__12_00418:250446519
TDr__12_00437:250446520
Tdr_97_00960:250398460
TDr__12_00432:250446522
TDr_12_00426:250446408
TDr__12_00219:250446530
TDr__13_00367:250446504
TDr__13_00458:250446507
TDr_13_00359:250446494
TDr__12_00171:250446535
TDr__12_00420:250446509
TDr__12_00430:250446524
TDr__12_00160:250446513
TDr_12_00433:250446409
TDr__12_00249:250446517
TDr__12_00438:250446533
TDr__13_00196:250446503
Tdr_08_00841:250446249
Tdr_09_00114:250446242
Tdr_08_00632:250446257
Tdr_08_00662__M_:250446255
Tdr_08_00621:250446264
Tdr_08_00648:250398455
Tdr_08_00185__M_:250446235
Tdr_08_00645:250446265
Tdr_08_00710:250446260
TDr__13_00189:250446477
TDr__13_00084:250446502
TDr__13_00208:250446490
Tdr_08_00669:250446243
Tdr_08_00705:250446246
Tdr_08_00733:250446229
TDr_2455:250446206
TDr__13_00198:250446497
TDr_13_00200:250446484
TDr_13_00227:250446483
TDr_89_00727:250446367
Omi_efun:250446190
Tdr_08_00810:250446193
Tdr_08_00122:250446244
Tdr_96_01818__M_:250446245
TDr_13_00391:250446495
TDr__13_00411:250446478
TDr__13_00421:250446498
Tdr_08_00017:250446256
TDr_08_00108:250446391
Tdr_08_01091:250446198
Tdr_99_02626:250446275
TDr_2974:250446220
Tdr_08_01046:250446221
Tdr_08_00098:250446281
TDr_12_00479:250446396
08_00963:250446323
Tdr_08_01016:250446279
Tdr_08_00133:250446197
Tdr_87_00211:250446250
Tdr_97_00940:250398446
Tdr_95_19177:250398448
Tdr_95_01958:250446266
TDr_95_19158:250446355
11_00263:250446335
Tdr_96_00582:250446208
TDr_12__00454:250446403
TDr__13_00288:250446482
TDr_12_00435:250446399
TDr_Ehuru:250446340
08_00896:250446318
TDr__13_00172:250446481
99_02354:250446325
Tdr_99_02789__M_:250446228
TDr__13_00256:250446500
TDr_3729:250398217
TDr_3647:250398477
TDr_3311:250398190
TDr_3647:250398212
Jirad_04_219:250398468
TDr_1707:250446317
TDr_2349:250398083
TDr_Amula:250398447
TDr__12_00422:250446526
TDr__12_00179:250446532
TDr__12_00250:250446512
TDr_3364:250378554
Tdr_89_02677:250446188
TDr_3524:250446460
TDr_3579:250446468
TDr__12_00195:250446531
TDr__12_00415:250446527
TDr__12_00423:250446514
TDr__12_00456:250446523
TDr__12_00429:250446528
TDr__12_00150:250446516
TDr__12_00168:250446534
TDr__12_00427:250446521
TDr_makakusa_m3H:250378500
Chk_TDr_89_02665:250378547
Tdr_89_02475:250398452
TDr_Ame_m3:250398140
Tdr_08_00082:250446239
Ufenyi:250446253
TDr_3765:250446203
Tdr_08_21_2:250446268
TDr_3518:250446351
TDr_1491:250446455
TDr_1709:250446372
TDr_2000:250446474
TDr_2440:250398078
TDr_2608:250398069
TDr_4070:250398464
TDr_1851:250398471
TDr_3576:250398497
TDr_2385:250398074
TDr_4172:250398516
TDr_1899:250378520
TDr_2880:250398192
TDr_2910:250398206
TDr_2553:250398055
TDr_2740:250398191
TDr_1905:250398263
TDr_2502:250398273
TDr_3484:250398238
TDr_3006:250398204
TDr_3527:250398210
TDr_3974:250398219
TDr_3543:250378585
TDr_4100:250398467
TDr_1850:250378517
TDr_1655:250378546
TDr_1657:250378544
TDr_4192:250398525
TDr_4031:250398523
TDr_3631:250398476
TDr_3643:250398478
TDr_2090:250398091
TDr_4178:250398526
TDr_3624:250398475
TDr_2572:250446373
TDr_1856:250378518
Tdr_08_00153:250405366
TDr_3600:250446219
TDr_1935:250378523
TDr_2744:250398500
TDr_1765:250446377
TDr_4173:250398524
Ogini_H5:250378504
Tdr_08_00108:250446213
Tdr_08_00176:250398366
Tdr_08_00014:250405350
Tdr_08_00155:250398384
Tdr_08_00040:250398401
Tdr_08_00229:250398403
Tdr_08_00122:250405347
Tdr_08_00130:250398334
Tdr_08_00161:250398398
Tdr_08_00115:250398346
Tdr_08_00092:250405354
Tdr_09_00385:250405325
Tdr_07_00732:250398400
Tdr_08_01692:250398340
Tdr_08_00207:250405341
Tdr_08_00218:250405339
Tdr_08_00041:250398341
Tdr_08_00194:250405346
Tdr_08_00254:250398396
Tdr_08_00141:250405334
Tdr_08_00071:250398339
Tdr_08_00134:250398338
Tdr_08_00094:250405381
TDr_12_00509:250446394
Tdr_09_00056:250398381
Tdr_09_00063:250398379
Tdr_09_00120:250398397
Tdr_09_00018:250398331
Tdr_09_00104:250398370
Tdr_09_00364:250398372
Tdr_09_00155:250405330
Tdr_09_00292:250398368
Tdr_09_00280:250405331
Tdr_09_00123:250398374
Tdr_09_00134:250405327
Tdr_09_00071:250405335
Tdr_08_00023:250405338
Tdr_09_00002:250398386
Tdr_09_00028:250398382
Tdr_09_00043:250405340
Tdr_09_00059:250398375
Tdr_09_00715:250398399
Tdr_09_00248:250405322
Tdr_09_00082:250405361
Tdr_09_00057:250398378
Tdr_09_00061:250398373
Tdr_09_00061:250398377
Tdr_09_00058:250398385
Tdr_09_00325:250398383
Tdr_08_01919:250405369
Tdr_09_00003:250405388
TDr_2756:250398247
TDr_3995:250398351
TDr_4173:250398357
TDr_3327:250398246
TDr_1798:250405296
TDr_2312__M_:250405378
TDr_1943:250405297
TDr_1813:250398239
TDr_3668:250398218
TDr_2247:250398318
TDr_3568:250398362
TDr_2630:250398322
TDr_2212:250398260
Tdr_89_02475:250398395
Hembakwase:250398134
TDr_2038:250398096
TDr_4078:250398221
TDr_4092:250398226
TDr__12_00419:250446511
TDr_2540:250398061
TDr_2285:250398359
TDr_2438:250398232
TDr_4185:250398223
TDr_2575:250398056
TDr_3881:250398350
Tdr_89_02617:250398321
Tdr_08_00662:250398342
Tdr_08_00789:250405342
Tdr_08_00861:250405344
Tdr_08_02381:250405349
Tdr_08_00841:250398337
Tdr_08_00669:250405337
TDr_12__00458:250446444
TDr_95_19177_B62:250398133
TDr_12_00429:250446406
TDr__12_00416:250446508
TDr_94_01108:250398127
TDr_97_01715:250398132
Tdr_08_00727:250405351
Tdr_97_00907:250405379
Tdr_99_02607:250405357
Tdr_99_02674:250398450
TDr_12_00475:250446400
Tdr_08_00924:250398367
Tdr_08_01464:250398343
Tdr_08_01024:250405372
Tdr_08_00998:250398402
Tdr_08_01123:250398344
Tdr_08_00926:250405326
Tdr_08_01085:250405373
TDr_00_0058_M4:250398128
Tdr_96_01395:250398445
Tdr_95_19158:250405358
Tdr_97_00903:250405329
TDr_00_00362:250398147
Tdr_02_00515:250398442
TDr_00_00539:250398142
TDr_96_01817:250398141
Tdr_08_00756:250405352
Tdr_08_00742:250405353
Tdr_08_00764__M_:250405380
Tdr_08_00898:250405333
Tdr_08_00639:250405363
Tdr_08_00641:250405364
Tdr_95_19158:250398371
TDr_96_00604B10:250398149
TDr_96_00604B7:250398139
Tdr_07_00157:250405328
Tdr_11_01036:250405324
Tdr_05_00632:250405343
jircas_99_00777:250405389
Tdr_08_00589:250398394
Tdr_95_00965:250405385
Tdr_08_00989:250398332
Tdr_08_01051:250398335
Tdr_08_01278:250398347
Tdr_08_00292:250405355
Tdr_99_02354:250398369
Tdr_o08_00882:250405323
Tdr_01_00405:250405359
Tdr_08_01344:250398345
Tdr_11_01041:250405332
Tdr_96_00629:250405383
TDr_12_00507:250446405
Tdr_96_00625:250398456
TDr_12_00408:250446407
TDr_12_00467:250446442
TDr_12_00474:250446410
TDr__13_00294:250446480
Tdr_97_00205:250398454
Tdr_09_00108:250446202
TDr__13_00415:250446493
TDr_12_00447:250446395
TDr_12_00478:250446404
Tdr_08_00126:250446259
TDr__13_00318:250446487
TDr_3477:250398242
TDr_2148:250405311
Tdr_11_00276:250398329
Tdr_08_00015:250398326
Tdr_08_01026:250398365
Tdr_08_00119:250398333
Tdr_08_00292:250398328
Tdr_09_00285:250398380
Tdr_08_00003:250405348
Tdr_08_01512:250398327
Tdr_08_00905:250398330
Tdr_08_01090:250405345
TDr_00_00180:250398137
TDr_River_Omuku_B4:250398150
Alumaco:250398392
TDr_3430:250378575
Ekiti_HB513:250398148
TDr_1913:250398264
TDr_3958:250398352
TDr_4091:250398356
TDr_2787:250398207
TDr_2163:250398088
TDr_2249:250398105
TDr_2491:250398066
TDr_1510:250405320
TDr_2369:250398231
TDr_2195:250405367
TDr_2029:250398098
TDr_2713:250398189
TDr_2041:250398225
TDr_4084:250398222
TDr_2453:250398080
TDr_2276:250405377
TDr_2674:250398240
TDr_2984:250398256
TDr_94_01108:250398364
TDr_2329:250398270
TDr_2083:250398312
TDr_2284:250398230
TDr_2390:250398268
TDr_2575:250398274
TDr_3842:250398390
TDr_95_19177:250398393
Tdr_99_02824:250405356
TDr_3814:250398391
TDr_3292:250398194
TDr_4154:250398228
TDr_3540:250398209
TDr_2050:250405298
TDr_3556:250398216
TDr_3598:250398215
TDr_2503:250398275
TDr_4029:250398354
TDr_2042:250398235
Keemi:250398146
TDr_1772:250405294
Tdr_08_00945:250398336
TDr_1556:250398123
TDr_2741:250398251
TDr_1953:250446456
TDr_2307:250398271
TDr_3483:250398201
TDr_2724:250398259
TDr_00_00196:250446346
TDr_1775:250446369
TDr_2425:250398267
TDr_2826:250446383
TDr_2028:250378505
TDr_2331:250398112
TDr_1449:250378510
TDr_1499:250398129

SNP matrix

SNP matrix
External data
In-house developed scripts

Chr10
Chr1
Chr4
Chr6
Chr5
Chr2
Chr3
Chr7
Chr8
Chr18
Chr9
Chr16
Chr17
Chr15
Chr13
Chr14
Chr12
Chr11
Cassava Assembly
& Annotation
Version 6.1

Cassava Assembly
& Annotation
Version 6.1
Gene Distribution
SNP Distribution
GBS Coverage
Heterocygosity

Transcriptomics (RNA-seq) mapping, assembly and expression profiling
What is RNA-seq?

smallRNA data analysis: discovery and expression profiling
Automated pipeline for reference supported and de
novo transcriptome assembly and expression profiling

Small RNA are short (21
-200nt) long RNA, not coding
for proteins with gene
regulatory effects.

Automated pipeline for non-coding RNA classification
and expression profiling.

DNA methylation (BS-seq) data analysis
What is BS-seq?
DNA methylation is
another gene regulation
mechanism which can be
inherited.

DNA (shotgun) assembly and variation calling
Genome annotation using different data pipelines and visualization

Reference data – Databases for existing data
Genomic Reference Data
Cassava (sequence, annotation, function)
D.rotundata (sequence, working on annotation and function)
D.alata (waiting for sequence and annotation)
Maize (ready sequence and annotation)
Banana (ready sequence and annotation)
Archive
Cassava (GBS, WGS, RNA-seq)
D.rotundata (GBS, smallRNA)
Maize (GBS)

INTERNET– connection to external Databases
Automated pipelines and strategies for big data
downloads

Bioinformatics & IITA
Development of Bioinformatics Capacity
IITA Projects
Involvement in planning of data production, analysis -
financing of data storage and analysis
Bioinformatics
Bioscience
Data analysis, Data repositories, Visualization

Bioinformatics & IITA
Development of Bioinformatics Capacity
In project with sequencing activities:
We need to individuate the bioinformatics part
We need to take over at least a part of the bioinformatics
activities
We have the Bioscience involved in the planning of the data
production to optimize the data analysis and knowledge building
Capacity building to enforce the bioinformatics facility

Thank you!
Data from:
Ranjana Bhattacharjee
Livia Stavolone
Morag Ferguson
Ismail Rabbi

Bioinformatics at IITA

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