TY - GEN
T1 - Genomic Compression with Decoder Alignment under Single Deletion and Multiple Substitutions
AU - Gershon, Yotam
AU - Cassuto, Yuval
N1 - Publisher Copyright: © 2022 IEEE.
PY - 2022
Y1 - 2022
N2 - We address the problem of compressing genomic read data produced by modern shotgun sequencing technologies, where a reference genome, closely similar to the sequenced one, is available only at the decoder. This problem, addressed by distributed source coding techniques, requires an alignment and validation layer in the decoder. In this work, we extend a previous work, to allow a single deletion along with the previously addressed multiple substitutions. The results include a new distance for efficient alignment under deletion and substitutions, a derivation of the exact distribution of this distance on random sequences, as well as procedures to recover the read from multiple invocations of a substitutions-only decoder.
AB - We address the problem of compressing genomic read data produced by modern shotgun sequencing technologies, where a reference genome, closely similar to the sequenced one, is available only at the decoder. This problem, addressed by distributed source coding techniques, requires an alignment and validation layer in the decoder. In this work, we extend a previous work, to allow a single deletion along with the previously addressed multiple substitutions. The results include a new distance for efficient alignment under deletion and substitutions, a derivation of the exact distribution of this distance on random sequences, as well as procedures to recover the read from multiple invocations of a substitutions-only decoder.
UR - http://www.scopus.com/inward/record.url?scp=85136312313&partnerID=8YFLogxK
U2 - https://doi.org/10.1109/ISIT50566.2022.9834472
DO - https://doi.org/10.1109/ISIT50566.2022.9834472
M3 - منشور من مؤتمر
T3 - IEEE International Symposium on Information Theory - Proceedings
SP - 998
EP - 1003
BT - 2022 IEEE International Symposium on Information Theory, ISIT 2022
T2 - 2022 IEEE International Symposium on Information Theory, ISIT 2022
Y2 - 26 June 2022 through 1 July 2022
ER -