TY  - JOUR
TI  - Detailed evaluation of cancer sequencing pipelines in different microenvironments and heterogeneity levels
AB  - The importance of next generation sequencing (NGS) rises in cancer research as accessing this key technology becomeseasier for researchers. The sequence data created by NGS technologies must be processed by various bioinformatics algorithms withina pipeline in order to convert raw data to meaningful information. Mapping and variant calling are the two main steps of these analysispipelines, and many algorithms are available for these steps. Therefore, detailed benchmarking of these algorithms in different scenariosis crucial for the efficient utilization of sequencing technologies. In this study, we compared the performance of twelve pipelines(three mapping and four variant discovery algorithms) with recommended settings to capture single nucleotide variants. We observedsignificant discrepancy in variant calls among tested pipelines for different heterogeneity levels in real and simulated samples withoverall high specificity and low sensitivity. Additional to the individual evaluation of pipelines, we also constructed and tested theperformance of pipeline combinations. In these analyses, we observed that certain pipelines complement each other much better thanothers and display superior performance than individual pipelines. This suggests that adhering to a single pipeline is not optimal forcancer sequencing analysis and sample heterogeneity should be considered in algorithm optimization.
AU  - ergün, mehmet arif
AU  - Sarıhan, Şahin
AU  - KISAKOL, Batuhan
AU  - baysan, mehmet
DO  - 10.3906/biy-2008-8
PY  - 2021
JO  - Turkish Journal of Biology
VL  - 45
IS  - 2
SN  - 1300-0152
SP  - 114
EP  - 126
DB  - TRDizin
UR  - http://search/yayin/detay/434803
ER  -