Illumina short-read sequencing data, de novo assembly and annotations of the Drosophila nasuta nasuta genome

Data in Brief - Tập 34 - Trang 106674 - 2021
Stafny DSouza1, Koushik Ponnanna1, Amruthavalli Chokkanna1, Nallur Ramachandra1
1Department of Studies in Genetics and Genomics, University of Mysore, Mysuru, India

Tài liệu tham khảo

Wilson, 1969, Cytogenetic relations in the Drosophila nasuta subgroup of the immigrans group of species, Univ. Texas Publ., 6918, 207 Ramachandra, 1986, The chromosomes of two Drosophila races: D. nasuta nasuta and D. nasuta albomicana, Chromosoma, 93, 243, 10.1007/BF00292744 Bachtrog, 2006, The speciation history of the Drosophila nasuta complex, Genet. Res., 88, 13, 10.1017/S0016672306008330 Mohanty, 2017, Genome-wide comparative analysis of four Indian Drosophila species, Mol. Genet. Genom., 292, 1197, 10.1007/s00438-017-1339-8 Kajitani, 2014, Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads, Genome Res., 24, 1384, 10.1101/gr.170720.113 Leszek, 2016, Redundans: an assembly pipeline for highly heterozygous genomes, Nucl. Acids Res., 44 Boetzer, 2011, Scaffolding pre-assembled contigs using SSPACE, Bioinformatics, 27, 578, 10.1093/bioinformatics/btq683 Boetzer, 2012, Toward almost closed genomes with GapFiller, Genome Biol., 13, R56, 10.1186/gb-2012-13-6-r56 Assembly-Stats: Assembly Metric Visualisations to Facilitate Rapid Assessment and Comparison of Assembly Quality. https://github.com/rjchallis/assembly-stats. Li, 2018, Minimap2: pairwise alignment for nucleotide sequences, Bioinformatics, 34, 3094, 10.1093/bioinformatics/bty191 Simão, 2015, BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs, Bioinformatics, 31, 3210, 10.1093/bioinformatics/btv351 Kurtz, 2004, Versatile and open software for comparing large genomes, Genome Biol., 5, R12, 10.1186/gb-2004-5-2-r12 Dot, An interactive Dot Plot Viewer For Genome-Genome Alignments. https://github.com/marianattestad/dot (accessed 08 September 2020) Campbell, 2014, MAKER-P: a tool kit for the rapid creation, management, and quality control of plant genome annotations, Plant Physiol., 164, 513, 10.1104/pp.113.230144 Palmer, 2017 Brůna, 2020, GeneMark-EP+: eukaryotic gene prediction with self-training in the space of genes and proteins, NAR Genom. Bioinform., 2, lqaa026, 10.1093/nargab/lqaa026 Chan P.P., Lowe T.M. tRNAscan-SE: searching for tRNA genes in genomic sequences. In: Kollmar M. (eds) Gene Prediction. Methods Mol. Biol. 1962 (2019) 1–14. Humana, New York, NY.10.1007/978-1-4939-9173-0_1 Altschul, 1990, Basic local alignment search tool, J. Mol. Biol., 215, 403, 10.1016/S0022-2836(05)80360-2 Wu, 2011, WebMGA: a customizable web server for fast metagenomic sequence analysis, BMC Genom., 12, 444, 10.1186/1471-2164-12-444 DSouza, 2020