Zobrazeno 1 - 10
of 5 596
pro vyhledávání: '"Read-alignment"'
Autor:
Egor Guguchkin, Artem Kasianov, Maksim Belenikin, Gaukhar Zobkova, Ekaterina Kosova, Vsevolod Makeev, Evgeny Karpulevich
Publikováno v:
BMC Bioinformatics, Vol 25, Iss 1, Pp 1-12 (2024)
Abstract Motivation Alignment of reads to a reference genome sequence is one of the key steps in the analysis of human whole-genome sequencing data obtained through Next-generation sequencing (NGS) technologies. The quality of the subsequent steps of
Externí odkaz:
https://doaj.org/article/5673c13f49cb427882fab0752bb16df8
Publikováno v:
Future Internet, Vol 16, Iss 6, p 217 (2024)
Sequence alignment is a critical factor in the variant analysis of genomic research. Since the FM (Ferrainas–Manzini) index was developed, it has proven to be a model in a compact format with efficient pattern matching and high-speed query searchin
Externí odkaz:
https://doaj.org/article/1fc16686ea474b0aaabc72cf80064f49
Autor:
Kristoffer Sahlin
Publikováno v:
Genome Biology, Vol 23, Iss 1, Pp 1-27 (2022)
Abstract Read alignment is often the computational bottleneck in analyses. Recently, several advances have been made on seeding methods for fast sequence comparison. We combine two such methods, syncmers and strobemers, in a novel seeding approach fo
Externí odkaz:
https://doaj.org/article/0cee7d1b8fad4cf5ac2ffd833ef576f3
Publikováno v:
Plants, Vol 13, Iss 5, p 582 (2024)
The utmost goal of selecting an RNA-Seq alignment software is to perform accurate alignments with a robust algorithm, which is capable of detecting the various intricacies underlying read-mapping procedures and beyond. Most alignment software tools a
Externí odkaz:
https://doaj.org/article/4521db2c748848368161e01151d201d5
Autor:
Dhrithi Deshpande, Karishma Chhugani, Yutong Chang, Aaron Karlsberg, Caitlin Loeffler, Jinyang Zhang, Agata Muszyńska, Viorel Munteanu, Harry Yang, Jeremy Rotman, Laura Tao, Brunilda Balliu, Elizabeth Tseng, Eleazar Eskin, Fangqing Zhao, Pejman Mohammadi, Paweł P. Łabaj, Serghei Mangul
Publikováno v:
Frontiers in Genetics, Vol 14 (2023)
RNA sequencing (RNA-seq) has become an exemplary technology in modern biology and clinical science. Its immense popularity is due in large part to the continuous efforts of the bioinformatics community to develop accurate and scalable computational t
Externí odkaz:
https://doaj.org/article/4d178d740d4d4435a387f270834537d2
Publikováno v:
F1000Research, Vol 8 (2022)
Read alignment is an important step in RNA-seq analysis as the result of alignment forms the basis for downstream analyses. However, recent studies have shown that published alignment tools have variable mapping sensitivity and do not necessarily ali
Externí odkaz:
https://doaj.org/article/8394df5fe09640d99f66ff9b88db85d9
Akademický článek
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Autor:
Jessica Bryant, Sebastian Baumgarten
Publikováno v:
Open Research Europe, Vol 2 (2022)
Background: The maintenance, regulation, and dynamics of heterochromatin in the human malaria parasite, Plasmodium falciparum, has drawn increasing attention due to its regulatory role in mutually exclusive virulence gene expression and the silencing
Externí odkaz:
https://doaj.org/article/77379df236524cb4918cd99dcbcaf84c
Autor:
Chi-Ming Leung, Dinghua Li, Yan Xin, Wai-Chun Law, Yifan Zhang, Hing-Fung Ting, Ruibang Luo, Tak-Wah Lam
Publikováno v:
BMC Genomics, Vol 21, Iss S6, Pp 1-9 (2020)
Abstract Background Next-generation sequencing (NGS) enables unbiased detection of pathogens by mapping the sequencing reads of a patient sample to the known reference sequence of bacteria and viruses. However, for a new pathogen without a reference
Externí odkaz:
https://doaj.org/article/69803fca3ca6439dbe50efc33aebce2f
Autor:
Avi Srivastava, Laraib Malik, Hirak Sarkar, Mohsen Zakeri, Fatemeh Almodaresi, Charlotte Soneson, Michael I. Love, Carl Kingsford, Rob Patro
Publikováno v:
Genome Biology, Vol 21, Iss 1, Pp 1-29 (2020)
Abstract Background The accuracy of transcript quantification using RNA-seq data depends on many factors, such as the choice of alignment or mapping method and the quantification model being adopted. While the choice of quantification model has been
Externí odkaz:
https://doaj.org/article/78912e03065e4f5e8d496ea17a6e5ae8