Optimizing variant calling performance for hotspot cases based on ion torrent sequencing technology / (Record no. 67673)
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| 000 -LEADER | |
|---|---|
| fixed length control field | 02594cam a2200337 a 4500 |
| 003 - CONTROL NUMBER IDENTIFIER | |
| control field | EG-GiCUC |
| 005 - DATE AND TIME OF LATEST TRANSACTION | |
| control field | 20250223032050.0 |
| 008 - FIXED-LENGTH DATA ELEMENTS--GENERAL INFORMATION | |
| fixed length control field | 180926s2018 ua h f m 000 0 eng d |
| 040 ## - CATALOGING SOURCE | |
| Original cataloging agency | EG-GiCUC |
| Language of cataloging | eng |
| Transcribing agency | EG-GiCUC |
| 041 0# - LANGUAGE CODE | |
| Language code of text/sound track or separate title | eng |
| 049 ## - LOCAL HOLDINGS (OCLC) | |
| Holding library | Deposite |
| 097 ## - Thesis Degree | |
| Thesis Level | M.Sc |
| 099 ## - LOCAL FREE-TEXT CALL NUMBER (OCLC) | |
| Classification number | Cai01.13.03.M.Sc.2018.Ba.O |
| 100 0# - MAIN ENTRY--PERSONAL NAME | |
| Personal name | Basma Nasser Abdelsalam Abdelfattah |
| 245 10 - TITLE STATEMENT | |
| Title | Optimizing variant calling performance for hotspot cases based on ion torrent sequencing technology / |
| Statement of responsibility, etc. | Basma Nasser Abdelsalam Abdelfattah ; Supervised Ayman M. Eldeib , Mohamed I. Abouelhoda |
| 246 15 - VARYING FORM OF TITLE | |
| Title proper/short title | تسريع تحديد الطفرات الجينية سابقة المعرفة لتكنولوجيا الايون توررنت |
| 260 ## - PUBLICATION, DISTRIBUTION, ETC. | |
| Place of publication, distribution, etc. | Cairo : |
| Name of publisher, distributor, etc. | Basma Nasser Abdelsalam Abdelfattah , |
| Date of publication, distribution, etc. | 2018 |
| 300 ## - PHYSICAL DESCRIPTION | |
| Extent | 68 P. : |
| Other physical details | facsimiles ; |
| Dimensions | 30cm |
| 502 ## - DISSERTATION NOTE | |
| Dissertation note | Thesis (M.Sc.) - Cairo University - Faculty of Engineering - Department of Systems and Biomedical Engineering |
| 520 ## - SUMMARY, ETC. | |
| Summary, etc. | In last few years, Next generation sequencing (NGS) revolutionized in DNA sequencing research. The latest major technologies released are Illumina and Ion torrent. In this study, we analyze the performance of calling variants using both platforms. In order to compare between both platforms, we used two sequenced data sets from ion community, which contain flow spaces required by Ion torrent. We are concerned with the execution time of both platforms. Ion torrent detects genome variants faster than Illumina but with low accuracy. Moreover, we found that Ion Torrent called slightly more variants but with higher false positive rate. The hotspot option provided by ion torrent variant caller provides more accurate variant calling positions as the filtration restricted to specific positions in the genome, but this leads to time consumption. Here, we enhanced the execution time to attain the accurate positive variants using torrent variant caller by using the NOCALL variants as hotspot regions to torrent variant caller (TVC). We developed two dependent packages the first one to create the new hotspot file (mHotspot) required by TVC and the second one to rerun the TVC with mHotspot file generated to get the exact positions of variants |
| 530 ## - ADDITIONAL PHYSICAL FORM AVAILABLE NOTE | |
| Additional physical form available note | Issued also as CD |
| 653 #4 - INDEX TERM--UNCONTROLLED | |
| Uncontrolled term | Ion torrent |
| 653 #4 - INDEX TERM--UNCONTROLLED | |
| Uncontrolled term | Next generation |
| 653 #4 - INDEX TERM--UNCONTROLLED | |
| Uncontrolled term | Variant calling |
| 700 0# - ADDED ENTRY--PERSONAL NAME | |
| Personal name | Ayman Mohamed Eldeib , |
| Relator term | |
| 700 0# - ADDED ENTRY--PERSONAL NAME | |
| Personal name | Mohamed Moustafa Ibrahim Abouelhoda , |
| Relator term | |
| 856 ## - ELECTRONIC LOCATION AND ACCESS | |
| Uniform Resource Identifier | <a href="http://172.23.153.220/th.pdf">http://172.23.153.220/th.pdf</a> |
| 905 ## - LOCAL DATA ELEMENT E, LDE (RLIN) | |
| Cataloger | Nazla |
| Reviser | Revisor |
| 905 ## - LOCAL DATA ELEMENT E, LDE (RLIN) | |
| Cataloger | Samia |
| Reviser | Cataloger |
| 942 ## - ADDED ENTRY ELEMENTS (KOHA) | |
| Source of classification or shelving scheme | Dewey Decimal Classification |
| Koha item type | Thesis |
| Source of classification or shelving scheme | Not for loan | Home library | Current library | Date acquired | Full call number | Barcode | Date last seen | Koha item type | Copy number |
|---|---|---|---|---|---|---|---|---|---|
| Dewey Decimal Classification | المكتبة المركزبة الجديدة - جامعة القاهرة | قاعة الرسائل الجامعية - الدور الاول | 11.02.2024 | Cai01.13.03.M.Sc.2018.Ba.O | 01010110076018000 | 22.09.2023 | Thesis | ||
| Dewey Decimal Classification | المكتبة المركزبة الجديدة - جامعة القاهرة | مخـــزن الرســائل الجـــامعية - البدروم | 11.02.2024 | Cai01.13.03.M.Sc.2018.Ba.O | 01020110076018000 | 22.09.2023 | CD - Rom | 76018.CD |