Author: Chen, Qi; Wang, Leyi; Zheng, Ying; Zhang, Jianqiang; Guo, Baoqing; Yoon, Kyoung-Jin; Gauger, Phillip C.; Harmon, Karen M.; Main, Rodger G.; Li, Ganwu
Title: Metagenomic analysis of the RNA fraction of the fecal virome indicates high diversity in pigs infected by porcine endemic diarrhea virus in the United States Document date: 2018_5_25
ID: 1nyhllij_33
Snippet: The comparable sensitivity and specificity between Kraken and Kaiju has also been studied previously [13] . Amino acid sequences are more conserved and are more tolerant to sequencing errors than underlying DNA, which may provide higher specificity (accuracy) to Kaiju program [13] . However, the sensitivity of Kaiju is concerned to be compromised by its inability to classify nucleic acid reads in non-coding region [13] . Therefore, we chose to us.....
Document: The comparable sensitivity and specificity between Kraken and Kaiju has also been studied previously [13] . Amino acid sequences are more conserved and are more tolerant to sequencing errors than underlying DNA, which may provide higher specificity (accuracy) to Kaiju program [13] . However, the sensitivity of Kaiju is concerned to be compromised by its inability to classify nucleic acid reads in non-coding region [13] . Therefore, we chose to use Kraken as our primary analysis program, and Kaiju program as our secondary confirmation method in the current study. It should be noted that a fecal sample negative for PEDV was not used as a negative control, which is one of our study limitations.
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