Browsing by Keywords "Read mapping"

Now showing items 1-8 of 8

    • Computational pan-genomics: status, promises and challenges 

      The Computational Pan-Genomics Consortium; Alkan, Can (Oxford University Press, 2018-01-01)
      Many disciplines, from human genetics and oncology to plant breeding, microbiology and virology, commonly face the challenge of analyzing rapidly increasing numbers of genomes. In case of Homo sapiens, the number of ...

    • A cryptocurrency incentivized voluntary grid computing platform for DNA read alignment 

      Özercan, Halil İbrahim (Bilkent University, 2019-09)
      The main computational bottleneck of High Throughput Sequencing (HTS) data analysis is to map the reads to a reference genome, for which clusters are typically used. However, building clusters large enough to handle ...

    • Distributed stream-processing framework for graph-based sequence alignment 

      Gökkaya, Alim Şükrücan (Bilkent University, 2020-01)
      Optimized the sequence alignment pipelines are needed to minimize the time required to complete processing the short-read genomic data. Today there are many sequence alignment tools exist, yet few of them are capable of ...

    • Fast and accurate mapping of complete genomics reads 

      Lee, D.; Hormozdiari, F.; Xin, H.; Hach, F.; Mutlu, O.; Alkan C. (Academic Press, 2015)
      Many recent advances in genomics and the expectations of personalized medicine are made possible thanks to power of high throughput sequencing (HTS) in sequencing large collections of human genomes. There are tens of ...

    • GateKeeper-GPU: accelerated pre-alignment filtering in short read mapping 

      Bingöl, Zülal (Bilkent University, 2020-08)
      Recent advances in high throughput sequencing (HTS) facilitate fast production of short DNA fragments (reads) in numerous amounts. Although the production is becoming inexpensive everyday, processing the present data for ...

    • GateKeeper-GPU: fast and accurate pre-alignment filtering in short read mapping 

      Bingöl, Zülal; Alser, Mohammed; Mutlu, Onur; Öztürk, Özcan; Alkan, Can (IEEE, 2021-06-24)
      We introduce GateKeeper-GPU, a fast and accurate pre-alignment filter that efficiently reduces the need for expensive sequence alignment. GateKeeper-GPU improves the filtering accuracy of GateKeeper, and by exploiting the ...

    • MAGNET: understanding and improving the accuracy of genome pre-alignment filtering 

      Alser, M.; Mutlu, O.; Alkan C. (I P S I, 2017)
      In the era of high throughput DNA sequencing (HTS) technologies, calculating the edit distance (i.e.,the minimum number of substitutions, insertions, and deletionsbetween a pair of sequences) forbillions of ...

    • SeGraM: A universal hardware accelerator for genomic sequence-to-graph and sequence-to-sequence mapping 

      Cali, D.Ş; Kanellopoulos, K.; Lindegger, J.; Bingöl, Zülal; Kalsi, G.S.; Zuo, Z.; Fırtına, Can; Cavlak, M.B.; Kim, J.; Ghiasi, N.M.; Singh, G.; Gómez-Luna, J.; Almadhoun Alserr, N.; Alser, M.; Subramoney, S.; Alkan, Can; Ghose, S.; Mutlu, O. (Association for Computing Machinery, 2020-06-11)
      A critical step of genome sequence analysis is the mapping of sequenced DNA fragments (i.e., reads) collected from an individual to a known linear reference genome sequence (i.e., sequence-to-sequence mapping). Recent works ...