scholarly journals Developmental validation of Oxford Nanopore Technology MinION sequence data and the NGSpeciesID bioinformatic pipeline for forensic genetic species identification

Author(s):  
Nina Vasiljevic ◽  
Marisa Lim ◽  
Emily Humble ◽  
Adeline Seah ◽  
Adelgunde Kratzer ◽  
...  
2007 ◽  
Vol 173 (1) ◽  
pp. 1-6 ◽  
Author(s):  
Nick Dawnay ◽  
Rob Ogden ◽  
Ross McEwing ◽  
Gary R. Carvalho ◽  
Roger S. Thorpe

2011 ◽  
Vol 152 (4) ◽  
pp. 1069-1073
Author(s):  
Timothée Bonnet ◽  
Per Kristian Slagsvold ◽  
Glenn-Peter Sætre

2021 ◽  
Vol 66 ◽  
pp. 403-425
Author(s):  
Wendylee Stott ◽  
Tom MacDougall ◽  
Edward F. Roseman ◽  
Stephen Lenart ◽  
Justin Chiotti ◽  
...  

ZooKeys ◽  
2019 ◽  
Vol 869 ◽  
pp. 147-160 ◽  
Author(s):  
Yaoyao Li ◽  
Haotian Li ◽  
Masaharu Motokawa ◽  
Yi Wu ◽  
Masashi Harada ◽  
...  

The Taiwanese gray shrew (Crocidura tanakae) and Asian gray shrew (C. attenuata) are so similar in size and morphology that the taxonomic status of the former has changed several times since its description; C. tanakae has also been regarded as an endemic species of Taiwan Island. In recent years, molecular identification has led to several reports of C. tanakae being distributed in the mainland of China. In this study, we determine the geographical distribution of C. attenuata and C. tanakae based on more than one hundred specimens collected during 2000 to 2018 over a wide area covering the traditional ranges of the two species in the mainland of China, and show a substantial revision of their distributions. Among 110 individuals, 33 C. attenuata and 77 C. tanakae were identified by Cytb gene and morphologies. Our results show, (1) C. attenuata and C. tanakae are distributed sympatrically in the mainland of China; (2) contrary to the previous reports, the distribution range of C. attenuata is restricted and much smaller than that of C. tanakae in the mainland of China; (3) Hainan Island, like Taiwan Island, is inhabited by C. tanakae only according to the present data.


2015 ◽  
Author(s):  
Sissel Juul ◽  
Fernando Izquierdo ◽  
Adam Hurst ◽  
Xiaoguang Dai ◽  
Amber Wright ◽  
...  

Whole genome sequencing on next-generation instruments provides an unbiased way to identify the organisms present in complex metagenomic samples. However, the time-to-result can be protracted because of fixed-time sequencing runs and cumbersome bioinformatics workflows. This limits the utility of the approach in settings where rapid species identification is crucial, such as in the quality control of food-chain components, or in during an outbreak of an infectious disease. Here we present What′s in my Pot? (WIMP), a laboratory and analysis workflow in which, starting with an unprocessed sample, sequence data is generated and bacteria, viruses and fungi present in the sample are classified to subspecies and strain level in a quantitative manner, without prior knowledge of the sample composition, in approximately 3.5 hours. This workflow relies on the combination of Oxford Nanopore Technologies′ MinION ™ sensing device with a real-time species identification bioinformatics application.


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