REFERENCES
Alonge, M., Soyk, S., Ramakrishnan, S., Wang, X., Goodwin, S., Sedlazeck, F. J., . . . Schatz, M. C. (2019). RaGOO: fast and accurate reference-guided scaffolding of draft genomes. Genome Biol, 20 (1), 224. doi:10.1186/s13059-019-1829-6
Bao, E., Jiang, T., & Girke, T. (2014). AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references.Bioinformatics, 30 (12), 319-328. doi:10.1093/bioinformatics/btu291
Berlin, K., Koren, S., Chin, C. S., Drake, J. P., Landolin, J. M., & Phillippy, A. M. (2015). Assembling large genomes with single-molecule sequencing and locality-sensitive hashing. Nature Biotechnology, 33 (6), 623-630. doi:10.1038/nbt.3238
Boetzer, M., & Pirovano, W. (2014). SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information. BMC Bioinformatics, 15 (1), 211. doi:10.1186/1471-2105-15-211
Bongartz, P. (2019). Resolving repeat families with long reads.BMC Bioinformatics, 20 (1), 232. doi:10.1186/s12859-019-2807-4
Bosi, E., Donati, B., Galardini, M., Brunetti, S., Sagot, M. F., Lio, P., . . . Fondi, M. (2015). MeDuSa: a multi-draft based scaffolder.Bioinformatics, 31 (15), 2443-2451. doi:10.1093/bioinformatics/btv171
Brunson, K., & Reich, D. (2019). The Promise of Paleogenomics Beyond Our Own Species. Trends in Genetics, 35 (5), 319-329. doi:10.1016/j.tig.2019.02.006
Chen, L., Qiu, Q., Jiang, Y., Wang, K., Lin, Z., Li, Z., . . . Wang, W. (2019). Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits. Science, 364 (6446), eaav6202. doi:doi:10.1126/science.aav6202
de Man, T. J., Stajich, J. E., Kubicek, C. P., Teiling, C., Chenthamara, K., Atanasova, L., . . . Gerardo, N. M. (2016). Small genome of the fungus Escovopsis weberi, a specialized disease agent of ant agriculture. Proc Natl Acad Sci U S A, 113 (13), 3567-3572. doi:10.1073/pnas.1518501113
Gordon, D., Huddleston, J., Chaisson, M. J. P., Hill, C. M., Kronenberg, Z. N., Munson, K. M., . . . Eichler, E. E. (2016). Long-read sequence assembly of the gorilla genome. Science, 352 (6281), aae0344. doi:doi:10.1126/science.aae0344
Grau, J. H., Hackl, T., Koepfli, K. P., & Hofreiter, M. (2018). Improving draft genome contiguity with reference-derived in silico mate-pair libraries. Gigascience, 7 (5). doi:10.1093/gigascience/giy029
Gurevich, A., Saveliev, V., Vyahhi, N., & Tesler, G. (2013). QUAST: quality assessment tool for genome assemblies. Bioinformatics, 29 (8), 1072-1075. doi:10.1093/bioinformatics/btt086
Iorizzo, M., Ellison, S., Senalik, D., Zeng, P., Satapoomin, P., Huang, J., . . . Simon, P. (2016). A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution. Nature Genetics, 48 (6), 657-666. doi:10.1038/ng.3565
Jain, M., Olsen, H. E., Paten, B., & Akeson, M. (2016). The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community. Genome Biol, 17 (1), 239. doi:10.1186/s13059-016-1103-0
Jarvis, D. E., Ho, Y. S., Lightfoot, D. J., Schmöckel, S. M., Li, B., Borm, T. J. A., . . . Tester, M. (2017). The genome of Chenopodium quinoa. Nature, 542 (7641), 307-312. doi:10.1038/nature21370
Kolmogorov, M., Raney, B., Paten, B., & Pham, S. (2014). Ragout-a reference-assisted assembly tool for bacterial genomes.Bioinformatics, 30 (12), i302-309. doi:10.1093/bioinformatics/btu280
Koren, S., Harhay, G. P., Smith, T. P., Bono, J. L., Harhay, D. M., McVey, S. D., . . . Phillippy, A. M. (2013). Reducing assembly complexity of microbial genomes with single-molecule sequencing.Genome Biol, 14 (9), R101. doi:10.1186/gb-2013-14-9-r101
Li, H. (2011). A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics, 27 (21), 2987-2993. doi:10.1093/bioinformatics/btr509
Li, H. (2013). Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv e-prints , arXiv:1303.3997.
Li, H. (2015). BFC: correcting Illumina sequencing errors.Bioinformatics, 31 (17), 2885-2887. doi:10.1093/bioinformatics/btv290
Lien, S., Koop, B. F., Sandve, S. R., Miller, J. R., Kent, M. P., Nome, T., . . . Davidson, W. S. (2016). The Atlantic salmon genome provides insights into rediploidization. Nature, 533 (7602), 200-205. doi:10.1038/nature17164
Loman, N. J., Quick, J., & Simpson, J. T. (2015). A complete bacterial genome assembled de novo using only nanopore sequencing data.Nature Methods, 12 (8), 733-735. doi:10.1038/nmeth.3444
Luo, R., Liu, B., Xie, Y., Li, Z., Huang, W., Yuan, J., . . . Wang, J. (2012). SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience, 1 (1), 18. doi:10.1186/2047-217X-1-18
Marçais, G., Delcher, A. L., Phillippy, A. M., Coston, R., Salzberg, S. L., & Zimin, A. (2018). MUMmer4: A fast and versatile genome alignment system. PLoS Comput Biol, 14 (1), e1005944. doi:10.1371/journal.pcbi.1005944
Marçais, G., & Kingsford, C. (2011). A fast, lock-free approach for efficient parallel counting of occurrences of k-mers.Bioinformatics, 27 (6), 764-770. doi:10.1093/bioinformatics/btr011
Maretty, L., Jensen, J. M., Petersen, B., Sibbesen, J. A., Liu, S., Villesen, P., . . . Schierup, M. H. (2017). Sequencing and de novo assembly of 150 genomes from Denmark as a population reference.Nature, 548 (7665), 87-91. doi:10.1038/nature23264
Pop, M., Phillippy, A., Delcher, A. L., & Salzberg, S. L. (2004). Comparative genome assembly. Briefings in Bioinformatics, 5 (3), 237-248. doi:10.1093/bib/5.3.237
Rasmussen, M., Li, Y., Lindgreen, S., Pedersen, J. S., Albrechtsen, A., Moltke, I., . . . Willerslev, E. (2010). Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature, 463 (7282), 757-762. doi:10.1038/nature08835
Rhoads, A., & Au, K. F. (2015). PacBio Sequencing and Its Applications.Genomics Proteomics & Bioinformatics, 13 (5), 278-289. doi:10.1016/j.gpb.2015.08.002
Rice, E. S., & Green, R. E. (2019). New Approaches for Genome Assembly and Scaffolding. Annual Review of Animal Biosciences, 7 (1), 17-40. doi:10.1146/annurev-animal-020518-115344
Sawyer, S., Krause, J., Guschanski, K., Savolainen, V., & Paabo, S. (2012). Temporal Patterns of Nucleotide Misincorporations and DNA Fragmentation in Ancient DNA. Plos One, 7 (3). doi:10.1371/journal.pone.0034131
Schmieder, R., & Edwards, R. (2011). Quality control and preprocessing of metagenomic datasets. Bioinformatics, 27 (6), 863-864. doi:10.1093/bioinformatics/btr026
Schneeberger, K., Ossowski, S., Ott, F., Klein, J. D., Wang, X., Lanz, C., . . . Weigel, D. (2011). Reference-guided assembly of four diverse Arabidopsis thaliana genomes. Proceedings of the National Academy of Sciences of the United States of America, 108 (25), 10249-10254. doi:10.1073/pnas.1107739108
Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V., & Zdobnov, E. M. (2015). BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics, 31 (19), 3210-3212. doi:10.1093/bioinformatics/btv351
Smadbeck, J. B., Johnson, S. H., Smoley, S. A., Gaitatzes, A., Drucker, T. M., Zenka, R. M., . . . Vasmatzis, G. (2018). Copy number variant analysis using genome-wide mate-pair sequencing. Genes Chromosomes & Cancer, 57 (9), 459-470. doi:10.1002/gcc.5
Stoneking, M., & Krause, J. (2011). Learning about human population history from ancient and modern genomes. Nature Reviews Genetics, 12 (9), 603-614. doi:10.1038/nrg3029
Tamazian, G., Dobrynin, P., Krasheninnikova, K., Komissarov, A., Koepfli, K. P., & O’Brien, S. J. (2016). Chromosomer: a reference-based genome arrangement tool for producing draft chromosome sequences.Gigascience, 5 (1), 1-11. doi:10.1186/s13742-016-0141-6
Tan, Y. Q., Tan, Y. Q., & Cheng, D. H. (2020). Whole-genome mate-pair sequencing of apparently balanced chromosome rearrangements reveals complex structural variations: two case studies. Molecular Cytogenetics, 13 (1), 15. doi:10.1186/s13039-020-00487-1
van Heesch, S., Kloosterman, W. P., Lansu, N., Ruzius, F.-P., Levandowsky, E., Lee, C. C., . . . Cuppen, E. (2013). Improving mammalian genome scaffolding using large insert mate-pair next-generation sequencing. BMC Genomics, 14 (1), 257. doi:10.1186/1471-2164-14-257
Wetzel, J., Kingsford, C., & Pop, M. (2011). Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies. BMC Bioinformatics, 12 (1), 95. doi:10.1186/1471-2105-12-95
TABLE 1 Statistics of the Clarias batrachus assemblies