The draft genome sequence and annotation of the desert woodrat Neotoma lepida

Genomics Data

Volumn 9, Issue , 2016, Pages 58-59

  Campbell, Michael ^a   Oakeson, Kelly F ^b   Yandell, Mark ^c   Halpert, James R ^d   Dearing, Denise ^b  

^a Cold Spring Harbor Laboratory ^*  (United States)

^b UNIVERSITY OF UTAH   (United States)

^c UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

^d UNIVERSITY OF CONNECTICUT   (United States)

Author keywords

Desert woodrat; Draft genome; Mammalian herbivore; Microbial detoxification; Toxic plant secondary compounds

Indexed keywords

LONG UNTRANSLATED RNA;

ANIMAL TISSUE; ARTICLE; DETOXIFICATION; GENE SEQUENCE; JUNIPERUS; JUNIPERUS MONOSPERMA; LARREA; LARREA TRIDENTATA; LIVER METABOLISM; MOLECULAR GENETICS; NEOTOMA; NEOTOMA LEPIDA; NONHUMAN; PRIORITY JOURNAL; RAT;

EID: 84976420313     PISSN: 22135960     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gdata.2016.06.008     Document Type: Article

References (12)

1. Zhbannikov I.Y., Hunter S.S., Settles M.L. Zhbannikov: SeqyClean User Manual - Google Scholar 2013.
2. Gnerre S., Maccallum I., Przybylski D., Ribeiro F.J., Burton J.N., Walker B.J., et al. High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc. Natl. Acad. Sci. U. S. A. 2011, 108:1513-1518. 10.1073/pnas.1017351108.
3. Bolger A.M., Lohse M., Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014, 30:2114-2120. 10.1093/bioinformatics/btu170.
4. Grabherr M.G., Haas B.J., Yassour M., Levin J.Z., Thompson D.A., Amit I., et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 2011, 29:644-652. 10.1038/nbt.1883.
5. Parra G., Bradnam K., Korf I. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics 2007, 23:1061-1067. 10.1093/bioinformatics/btm071.
6. Bao W., Kojima K.K., Kohany O. Repbase update, a database of repetitive elements in eukaryotic genomes. Mob. DNA 2015, 6:1. 10.1186/s13100-015-0041-9.
7. A. Smit, R. Hubley, P. Green, 2010 RepeatMasker Open-3.0, URL: , 1996. http://www.repeatmasker.org.
8. Cantarel B.L., Korf I., Robb S.M.C., Parra G., Ross E., Moore B., et al. MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res. 2008, 18:188-196. 10.1101/gr.6743907.
9. Campbell M.S., Holt C., Moore B., Yandell M. Genome Annotation and Curation Using MAKER and MAKER-P 2014, John Wiley & Sons, Inc., Hoboken, NJ, USA. 10.1002/0471250953.bi0411s48.
10. Campbell M.S., Law M., Holt C., Stein J.C., Moghe G.D., Hufnagel D.E., et al. MAKER-P: a tool kit for the rapid creation, management, and quality control of plant genome annotations. Plant Physiol. 2014, 164:513-524. 10.1104/pp.113.230144.
11. Holt C., Yandell M. MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. BMC Bioinformatics 2011, 12:1. 10.1186/1471-2105-12-491.
12. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 1990, 215:403-410. 10.1016/S0022-2836(05)80360-2.