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contributes to widespread intron retention in plants. Nature Plants,
6(7), 780–788.
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L., Pan, Q., Nachman, E. N., Alipanahi, B., Gonatopoulos-Pournatzis, T.,
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Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., &amp; Durbin,
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Bioinformatics, 25(16), 2078–2079.
https://doi.org/10.1093/bioinformatics/btp352</unstructured_citation>
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<doi>10.1038/nmeth.3317</doi>
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F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., &amp;
Gingeras, T. R. (2013). STAR: Ultrafast universal RNA-seq aligner.
Bioinformatics, 29(1), 15–21.
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F., Hugenholtz, P., &amp; Tyson, G. W. (2012). Grinder: A versatile
amplicon and shotgun sequence simulator. Nucleic Acids Research, 40(12),
e94–e94. https://doi.org/10.1093/nar/gks251</unstructured_citation>
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D. H. (2015). Fast and sensitive protein alignment using DIAMOND. Nature
Methods, 12(1), 59.
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<article_title>De novo transcript sequence reconstruction
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analysis</article_title>
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Yassour, M., Grabherr, M., Blood, P. D., Bowden, J., Couger, M. B.,
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sequence reconstruction from RNA-seq using the trinity platform for
reference generation and analysis. Nature Protocols, 8(8),
1494.</unstructured_citation>
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<article_title>GFF/GTF parsing utility providing format
conversions, region filtering, FASTA sequence extraction and
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<unstructured_citation>Pertea, G. (2019). GFF/GTF parsing
utility providing format conversions, region filtering, FASTA sequence
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