GenomeTools: A Comprehensive Software Library for Efficient Processing of Structured Genome Annotations
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Cites background from "GenomeTools: A Comprehensive Softwa..."
...LTRharvest (Ellinghaus et al., 2008) is part of GenomeTools version 1.5.4 (Gremme et al., 2013)....
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Cites background or methods from "GenomeTools: A Comprehensive Softwa..."
...…to a stool sample from a child in Mexico with diarrhea (Yu et al. 2012), a nasal swab sample from a patient with acute respiratory illness (Greninger et al. 2010), and a serum sample from a patient in California with hantavirus pulmonary syndrome (Nunez et al. 2014), harboring RSV,…...
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...…a nasal swab sample pool from patients infected with 2009 pandemic in- fluenza H1N1 [influenza A(H1N1)pdm09] and sequenced using short 65-bp reads (Greninger et al. 2010), and (3) a serum sample from a patient with hantavirus pulmonary syndrome from Sin appropriate empirical cutoff for SNAP…...
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...…the most widely used approach is computational subtraction of reads corresponding to the host (e.g., human), followed by alignment to reference databases that contain sequences from candidate pathogens (MacConaill and Meyerson 2008; Greninger et al. 2010; Kostic et al. 2011; Zhao et al. 2013)....
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References
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