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Axe: rapid, competitive sequence read demultiplexing using a trie [article]

Kevin D. Murray, Justin O. Borevitz
2017 bioRxiv   pre-print
Here we implement a rapid algorithm for demultiplexing DNA sequence reads with in-read indixces. Axe selects the optimal index present in a sequence read, even in the presence of sequencing errors.  ...  The algorithm is able to handle combinatorial indexing, indices of differing length, and several mismatches per index sequence.  ...  This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PUR-POSE.  ... 
doi:10.1101/160606 fatcat:dk4vkbg4anhd3hjp6ryurgrr4q

Axe: rapid, competitive sequence read demultiplexing using a trie

Kevin D Murray, Justin O Borevitz, Bonnie Berger
2018 Bioinformatics  
Here we implement a rapid algorithm for demultiplexing DNA sequence reads with in-read indices. Axe selects the optimal index present in a sequence read, even in the presence of sequencing errors.  ...  The algorithm is able to handle combinatorial indexing, indices of differing length, and several mismatches per index sequence.  ...  Axe then associates each of these sequences with its respective sample identifier using a double-array trie.  ... 
doi:10.1093/bioinformatics/bty432 pmid:29868827 fatcat:xsfzvp2isrdijjunulqfb4oaoa

Supplemental Material for Friis et al., 2020

Guillermo Friis, Joel Vizueta, Edward G. Smith, David R. Nelson, Basel Krhaiwesh, Enas Qudeimat, Kourosh Salehi-Ashtiani, Alejandra Ortega, Alyssa Marshell, Carlos M. Duarte, John A. Burt
2020
Supplementary Information for the the publication "A high-quality genome assembly and annotation of the gray mangrove, Avicennia marina".  ...  Axe: rapid, competitive sequence read demultiplexing using 507 a trie. bioRxiv, 160606.508 Putnam, N.H., O'Connell, B.L., Stites, J.C., Rice, B.J., Blanchette, M., Calef, R., Troll, C.J., 509 Fields, A  ...  Axe: rapid, competitive sequence read demultiplexing using 537 a trie. bioRxiv, 160606.538 Putnam, N.H., O'Connell, B.L., Stites, J.C., Rice, B.J., Blanchette, M., Calef, R., Troll, C.J., 539 Fields, A  ... 
doi:10.25387/g3.13270154.v1 fatcat:3wmnfnrnyna6zi7ubpphnp23vi

New computational methods and plant models for evolutionary genomics [article]

Kevin Murray, University, The Australian National, University, The Australian National
2019
Axe, a short read sequence demultiplexer, demultiplexes samples from multiplexed GBS sequencing datasets. I show Axe has high accuracy, and outperforms previously published software.  ...  In Chapter 4, I develop kWIP, a de novo estimator of genetic distance. kWIP enables rapid estimation of genetic distances directly from sequence reads.  ...  Chapter 2 Axe: rapid, competitive sequence read demultiplexing using a trie Interest: none declared.  ... 
doi:10.25911/5d5148dd2e8ba fatcat:k3bjuwp3pjaczeihnqz2coqkzq

Future trends in microelectronics - reflections on the road to nanotechnology

1997 Precision engineering  
A change in social values amongst the rest of us might, in turn, go a long way helping us retaining our global competitiveness. Finally, we must recognize that our Ph.D.'  ...  A rather state-of-the-art description of the process sequences needed to construct such a 3-dimensional wiring structure is given in Table 1 .  ...  References Modern crystal growth methods allow multilayer heterostructures to be incorporated in a variety of novel and useful devices.  ... 
doi:10.1016/0141-6359(97)90048-9 fatcat:j7blw4wn6zbitmoqqffj46g54e

The genetic and demographic impacts of contemporary disturbance regimes in mountain ash forests [article]

Brenton Von Takach Dukai, University, The Australian National, University, The Australian National
2019
In south-eastern Australia, these factors are causing the rapid ecosystem collapse of montane forests.  ...  Timber harvesting, frequent wildfires and a changing climate are influencing ecosystem composition, structure and function globally, with resulting losses to biodiversity and economic indicators.  ...  BvTD was supported by a Lesslie Research Grant in Landscape Conservation and Ecology and an Ignition Project grant from the Centre for Biodiversity Analysis.  ... 
doi:10.25911/5d820ac04e269 fatcat:6y44s6t7fra6zcwgzbfixi2fdm