1 code implementation • 22 Jan 2023 • Can Firtina, Nika Mansouri Ghiasi, Joel Lindegger, Gagandeep Singh, Meryem Banu Cavlak, Haiyu Mao, Onur Mutlu
An important feature of nanopore sequencing, Read Until, can eject strands from sequencers without fully sequencing them, which provides opportunities to computationally reduce the sequencing time and cost.
1 code implementation • 9 Dec 2022 • Meryem Banu Cavlak, Gagandeep Singh, Mohammed Alser, Can Firtina, Joël Lindegger, Mohammad Sadrosadati, Nika Mansouri Ghiasi, Can Alkan, Onur Mutlu
However, for many applications, the majority of reads do no match the reference genome of interest (i. e., target reference) and thus are discarded in later steps in the genomics pipeline, wasting the basecalling computation.
1 code implementation • 20 Jul 2022 • Can Firtina, Kamlesh Pillai, Gurpreet S. Kalsi, Bharathwaj Suresh, Damla Senol Cali, Jeremie Kim, Taha Shahroodi, Meryem Banu Cavlak, Joel Lindegger, Mohammed Alser, Juan Gómez Luna, Sreenivas Subramoney, Onur Mutlu
When we analyze the state-of-the-art works, we find that there is a pressing need for a flexible, high-performant, and energy-efficient hardware-software co-design to efficiently and effectively solve all the major inefficiencies in the Baum-Welch algorithm for pHMMs.
1 code implementation • 17 Jan 2022 • Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak, Damla Senol Cali, Can Alkan, Onur Mutlu
Also available in Bioconda at: https://anaconda. org/bioconda/fastremap-bio.
1 code implementation • 18 Dec 2019 • Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak, Damla Senol Cali, Mohammed Alser, Nastaran Hajinazar, Can Alkan, Onur Mutlu
There are several tools that attempt to accelerate the process of updating a read data set from one reference to another (i. e., remapping).