Bioinformatics at IITA
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The document discusses bioinformatics at the International Institute of Tropical Agriculture (IITA). It defines bioinformatics and describes the large amount of biological data that is now available, including sequences, structures, and expressions. It then outlines IITA's bioinformatics resources, including personnel, computing hardware, and software tools for analyzing different types of biological data like genotyping by sequencing (GBS) and RNA sequencing. Specific IITA projects involving the analysis of cassava, yam, and other crop sequencing data are also mentioned.
Bioinformatics at IITA
- 1. www.iita.orgA member of CGIAR consortium Bioinformatics @ IITA Andreas Gisel IITA – Bioscience & Bioinformatics
- 2. www.iita.orgA member of CGIAR consortium Bioinformatics @ IITA Bioinformatics – definition and introduction Bioinformatics @ IITA Bioinformatics & IITA
- 3. www.iita.orgA member of CGIAR consortium Bioinformatics - definition Bio – Biology, Life Sciences Informatics – computational sciences DATA INTERPRETATIONS RESULTS Bio informatics
- 4. www.iita.orgA member of CGIAR consortium Bioinformatics - definition Bio – Biology, Life Sciences Informatics – computational sciences DATA INTERPRETATIONS RESULTS Data Repositories Knowledge
- 5. www.iita.orgA member of CGIAR consortium Bioinformatics - definition Bio – Biology, Life Sciences Informatics – computational sciences DATA INTERPRETATIONS 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.
- 6. www.iita.orgA member of CGIAR consortium ? Biological Data Descriptions Pictures
- 7. www.iita.orgA member of CGIAR consortium Descriptions Pictures Sequences Biological Data
- 8. www.iita.orgA member of CGIAR consortium 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
- 9. www.iita.orgA member of CGIAR consortium Descriptions Pictures Sequences Protein RNA DNA Structures Biological Data
- 10. www.iita.orgA member of CGIAR consortium Descriptions Pictures Sequences Protein RNA DNA Structures Protein RNA Biological Data
- 11. www.iita.orgA member of CGIAR consortium Descriptions Pictures Sequences Protein RNA DNA Structures Protein RNA Interactions Biological Data
- 12. www.iita.orgA member of CGIAR consortium Descriptions Pictures Sequences Protein RNA DNA Structures Protein RNA Interactions Expressions Biological Data
- 13. www.iita.orgA member of CGIAR consortium 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)
- 14. www.iita.orgA member of CGIAR consortium Descriptions Pictures Sequences Protein RNA DNA Structures Protein RNA Interactions Expressions Data Explosion
- 15. www.iita.orgA member of CGIAR consortium 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
- 16. www.iita.orgA member of CGIAR consortium 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
- 17. www.iita.orgA member of CGIAR consortium Bioinformatics @ IITA 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
- 18. www.iita.orgA member of CGIAR consortium Bioinformatics @ IITA 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.
- 19. www.iita.orgA member of CGIAR consortium Bioinformatics @ IITA Tools – Programs that process your data 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
- 20. www.iita.orgA member of CGIAR consortium Bioinformatics @ IITA Tools – Programs that process your data 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)
- 21. www.iita.orgA member of CGIAR consortium Bioinformatics @ IITA Tools – Programs that process your data GBS (genotyping by sequencing) data analysis and SNP calling
- 22. www.iita.orgA member of CGIAR consortium GBS (genotyping by sequencing) data analysis and SNP calling Ismail Rabbi Bioinformatics @ IITA Tools – Programs that process your data SNP matrix Cornell
- 23. www.iita.orgA member of CGIAR consortium Bioinformatics @ IITA Tools – Programs that process your data GBS (genotyping by sequencing) data analysis and SNP calling SNP matrix In-house
- 24. www.iita.orgA member of CGIAR consortium Bioinformatics @ IITA Tools – Programs that process your data GBS (genotyping by sequencing) data analysis and SNP calling SNP matrix Histogram of IBS.num Distance (1 PSA)− Frequency 0.00 0.05 0.10 0.15 0.20 0.25 01000200030004000
- 25. www.iita.orgA member of CGIAR consortium Bioinformatics @ IITA Tools – Programs that process your data GBS (genotyping by sequencing) data analysis and SNP calling 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 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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
- 26. www.iita.orgA member of CGIAR consortium Bioinformatics @ IITA Tools – Programs that process your data GBS (genotyping by sequencing) data analysis and SNP calling SNP matrix
- 27. www.iita.orgA member of CGIAR consortium Bioinformatics @ IITA Tools – Programs that process your data GBS (genotyping by sequencing) data analysis and SNP calling SNP matrix External data In-house developed scripts
- 28. www.iita.orgA member of CGIAR consortium GBS (genotyping by sequencing) data analysis and SNP calling Bioinformatics @ IITA Tools – Programs that process your data Chr10 Chr1 Chr4 Chr6 Chr5 Chr2 Chr3 Chr7 Chr8 Chr18 Chr9 Chr16 Chr17 Chr15 Chr13 Chr14 Chr12 Chr11 Cassava Assembly & Annotation Version 6.1
- 29. www.iita.orgA member of CGIAR consortium Cassava Assembly & Annotation Version 6.1 GBS (genotyping by sequencing) data analysis and SNP calling Bioinformatics @ IITA Tools – Programs that process your data Gene Distribution SNP Distribution GBS Coverage Heterocygosity
- 30. www.iita.orgA member of CGIAR consortium GBS (genotyping by sequencing) data analysis and SNP calling Bioinformatics @ IITA Tools – Programs that process your data
- 31. www.iita.orgA member of CGIAR consortium Bioinformatics @ IITA Tools – Programs that process your data Transcriptomics (RNA-seq) mapping, assembly and expression profiling What is RNA-seq?
- 32. www.iita.orgA member of CGIAR consortium Bioinformatics @ IITA Tools – Programs that process your data smallRNA data analysis: discovery and expression profiling Automated pipeline for reference supported and de novo transcriptome assembly and expression profiling
- 33. www.iita.orgA member of CGIAR consortium Bioinformatics @ IITA Tools – Programs that process your data smallRNA data analysis: discovery and expression profiling Small RNA are short (21 -200nt) long RNA, not coding for proteins with gene regulatory effects.
- 34. www.iita.orgA member of CGIAR consortium Bioinformatics @ IITA Tools – Programs that process your data smallRNA data analysis: discovery and expression profiling Automated pipeline for non-coding RNA classification and expression profiling.
- 35. www.iita.orgA member of CGIAR consortium Bioinformatics @ IITA Tools – Programs that process your data DNA methylation (BS-seq) data analysis What is BS-seq? DNA methylation is another gene regulation mechanism which can be inherited.
- 36. www.iita.orgA member of CGIAR consortium Bioinformatics @ IITA Tools – Programs that process your data DNA methylation (BS-seq) data analysis What is BS-seq? DNA methylation is another gene regulation mechanism which can be inherited.
- 37. www.iita.orgA member of CGIAR consortium Bioinformatics @ IITA Tools – Programs that process your data DNA (shotgun) assembly and variation calling Genome annotation using different data pipelines and visualization
- 38. www.iita.orgA member of CGIAR consortium Bioinformatics @ IITA 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)
- 39. www.iita.orgA member of CGIAR consortium Bioinformatics @ IITA 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)
- 40. www.iita.orgA member of CGIAR consortium Bioinformatics @ IITA 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)
- 41. www.iita.orgA member of CGIAR consortium Bioinformatics @ IITA INTERNET– connection to external Databases Automated pipelines and strategies for big data downloads
- 42. www.iita.orgA member of CGIAR consortium 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
- 43. www.iita.orgA member of CGIAR consortium 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
- 44. www.iita.orgA member of CGIAR consortium Thank you! Data from: Ranjana Bhattacharjee Livia Stavolone Morag Ferguson Ismail Rabbi