Draft Genome of the Insect-Parasitic Nematode Bradynema listronoti

Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. 1990. Basic local alignment search tool. Journal of Molecular Biology 215:403–410. Altschul S. F. Gish W. Miller W. Myers E. W. and Lipman D. J. 1990 Basic local alignment search tool Journal of Molecular Biology 215403 41010.1016/S0022-2836(05)80360-22231712Search in Google Scholar

Barnett, D. W., Garrison, E. K., Quinlan, A. R., Strömberg, M. P., and Marth, G. T. 2011. BamTools: a C++ API and toolkit for analyzing and managing BAM files. Bioinformatics 27:1691–1692 Barnett D. W. Garrison E. K. Quinlan A. R. Strömberg M. P. and Marth G. T. 2011 BamTools: a C++ API and toolkit for analyzing and managing BAM files Bioinformatics 271691 169210.1093/bioinformatics/btr174310618221493652Search in Google Scholar

Bruna, T., Hoff, K. J., Lomsadze, A., Stanke, M., and Borodovsky, M. 2021. BRAKER2: Automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS Supported by a Protein Database. NAR Genomics and Bioinformatics 3:lqaa108. Bruna T. Hoff K. J. Lomsadze A. Stanke M. and Borodovsky M. 2021 BRAKER2: Automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS Supported by a Protein Database NAR Genomics and Bioinformatics 3lqaa10810.1093/nargab/lqaa108778725233575650Search in Google Scholar

Challis, R., Richards, E., Rajan, J., Cochrane, G., and Blaxter, M. 2020. BlobToolKit – Interactive quality assessment of genome assemblies. G3 Genes|Genomes|Genetics 10:1361–1374. Challis R. Richards E. Rajan J. Cochrane G. and Blaxter M. 2020 BlobToolKit – Interactive quality assessment of genome assemblies G3 Genes|Genomes|Genetics 101361 137410.1534/g3.119.400908714409032071071Search in Google Scholar

Chen, S., Zhou, Y., Chen, Y., and Gu, J. 2018. fastp: An ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34:i884–i890. Chen S. Zhou Y. Chen Y. and Gu J. 2018 fastp: An ultra-fast all-in-one FASTQ preprocessor Bioinformatics 34i884 i89010.1093/bioinformatics/bty560612928130423086Search in Google Scholar

Gagnon, A.-È., Boivin, G., Bélair, G., and Mimee, B. 2019. Prevalence of a nematode castrator of the carrot weevil and impact on fecundity and survival. Parasitology 146:702–707. Gagnon A.-È. Boivin G. Bélair G. and Mimee B. 2019 Prevalence of a nematode castrator of the carrot weevil and impact on fecundity and survival Parasitology 146702 70710.1017/S003118201800205630567618Search in Google Scholar

Haghshenas, E., Asghari, H., Stoye, J., Chauve, C., and Hach, F. 2020. HASLR: Fast hybrid assembly of long reads. Cold Spring Harbor Laboratory. doi/10.1101/2020.01.27.921817. Haghshenas E. Asghari H. Stoye J. Chauve C. and Hach F. 2020 HASLR: Fast hybrid assembly of long reads. Cold Spring Harbor Laboratory. doi/10.1101/2020.01.27.92181710.1101/2020.01.27.921817Search in Google Scholar

Hoff, K. J., Lange, S., Lomsadze, A., Borodovsky, M., and Stanke, M. 2016. BRAKER1: Unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS. Bioinformatics 32:767–769. Hoff K. J. Lange S. Lomsadze A. Borodovsky M. and Stanke M. 2016 BRAKER1: Unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS Bioinformatics 32767 76910.1093/bioinformatics/btv661607816726559507Search in Google Scholar

Hoff, K. J., Lomsadze, A., Borodovsky, M., and Stanke, M. 2019. Whole-genome annotation with BRAKER. Methods in Molecular Biology 1962:65–95. Hoff K. J. Lomsadze A. Borodovsky M. and Stanke M. 2019 Whole-genome annotation with BRAKER Methods in Molecular Biology 196265 9510.1007/978-1-4939-9173-0_5663560631020555Search in Google Scholar

Kolmogorov, M., Yuan, J., Lin, Y., and Pevzner, P. A. 2019. Assembly of long, error-prone reads using repeat graphs. Nature Biotechnology 37:540–546. Kolmogorov M. Yuan J. Lin Y. and Pevzner P. A. 2019 Assembly of long, error-prone reads using repeat graphs Nature Biotechnology 37540 54610.1038/s41587-019-0072-830936562Search in Google Scholar

Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R.; and 1000 Genome Project Data Processing Subgroup. 2009. The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079. Li H. Handsaker B. Wysoker A. Fennell T. Ruan J. Homer N. Marth G. Abecasis G. Durbin R. and 1000 Genome Project Data Processing Subgroup. 2009. The sequence alignment/map format and SAMtools. Bioinformatics 252078 207910.1093/bioinformatics/btp352272300219505943Search in Google Scholar

Lomsadze, A., Burns, P. D., and Borodovsky, M. 2014. Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm. Nucleic Acids Research 42:e119. Lomsadze A. Burns P. D. and Borodovsky M. 2014 Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm Nucleic Acids Research 42e11910.1093/nar/gku557415075724990371Search in Google Scholar

Manni, M., Berkeley, M. R., Seppey, M., Simão, F. A., and Zdobnov, E. M. 2021. BUSCO update: Novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. Molecular Biology and Evolution 38:4647–4654. Manni M. Berkeley M. R. Seppey M. Simão F. A. and Zdobnov E. M. 2021 BUSCO update: Novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes Molecular Biology and Evolution 384647 465410.1093/molbev/msab199847616634320186Search in Google Scholar

Smit, A., Hubley, R., and Green, P. 2015. RepeatMasker Open-4.0. 2013–2015. Institute for Systems Biology. Available at: http://repeatmasker.org. Smit A. Hubley R. and Green P. 2015 RepeatMasker Open-4.0. 2013–2015. Institute for Systems Biology. Available at: http://repeatmasker.org.Search in Google Scholar

Song, L., Shankar, D. S., and Florea, L. 2016. Rascaf: Improving genome assembly with RNA sequencing data. The Plant Genome 9(3):1–12. Song L. Shankar D. S. and Florea L. 2016 Rascaf: Improving genome assembly with RNA sequencing data The Plant Genome 9 31 1210.3835/plantgenome2016.03.002727902792Search in Google Scholar

Stanke, M., Diekhans, M., Baertsch, R., and Haussler, D. 2008. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics 24:637–644. Stanke M. Diekhans M. Baertsch R. and Haussler D. 2008 Using native and syntenically mapped cDNA alignments to improve de novo gene finding Bioinformatics 24637 64410.1093/bioinformatics/btn01318218656Search in Google Scholar

Stanke, M., Schöffmann, O., Morgenstern, B., and Waack, S. 2006. Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC Bioinformatics 7:62. Stanke M. Schöffmann O. Morgenstern B. and Waack S. 2006 Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources BMC Bioinformatics 76210.1186/1471-2105-7-62140980416469098Search in Google Scholar

Ste-Croix, D. T., St-Marseille, A. F. G., Lord, E., Bélanger, R. R., Brodeur, J., and Mimee, B. 2021. Genomic profiling of virulence in the soybean cyst nematode using single-nematode sequencing. Phytopathology 111:137–148. Ste-Croix D. T. St-Marseille A. F. G. Lord E. Bélanger R. R. Brodeur J. and Mimee B. 2021 Genomic profiling of virulence in the soybean cyst nematode using single-nematode sequencing Phytopathology 111137 14810.1094/PHYTO-08-20-0348-FI33100145Search in Google Scholar

Vurture, G. W., Sedlazeck, F. J., Nattestad, M., Underwood, C. J., Fang, H., Gurtowski, J., and Schatz, M. C. 2017. GenomeScope: Fast reference-free genome profiling from short reads. Bioinformatics 33:2202–2204. Vurture G. W. Sedlazeck F. J. Nattestad M. Underwood C. J. Fang H. Gurtowski J. and Schatz M. C. 2017 GenomeScope: Fast reference-free genome profiling from short reads Bioinformatics 332202 220410.1093/bioinformatics/btx153587070428369201Search in Google Scholar

Walker, B. J., Abeel, T., Shea, T., Priest, M., Abouelliel, A., Sakthikumar, S., Cuomo, C. A., Zeng, Q., Wortman, J., Young, S. K., and Earl, A. M. 2014. Pilon: An integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE 9:e112963. Walker B. J. Abeel T. Shea T. Priest M. Abouelliel A. Sakthikumar S. Cuomo C. A. Zeng Q. Wortman J. Young S. K. and Earl A. M. 2014 Pilon: An integrated tool for comprehensive microbial variant detection and genome assembly improvement PLoS ONE 9e11296310.1371/journal.pone.0112963423734825409509Search in Google Scholar

Warren, R. L., Yang, C., Vandervalk, B. P., Behsaz, B., Lagman, A., Jones, S. J M., and Birol, I. 2015. LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads. GigaScience 4:35. doi/10.1186/ s13742-015-0076-3 Warren R. L. Yang C. Vandervalk B. P. Behsaz B. Lagman A. Jones S. J M. and Birol I. 2015 LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads GigaScience 435 doi/10.1186/ s13742-015-0076-310.1186/s13742-015-0076-3452400926244089Search in Google Scholar

Zeng, Y., Giblin-Davis, R., Bélair, G., Boivin, G., and Thomas, K. 2007. Bradynema listronoti n. sp. (Nematoda: Allantonematidae), a parasite of the carrot weevil Listronotus oregonensis (Coleoptera: Curculionidae) in Quebec, Canada. Nematology 9:608–622. Zeng Y. Giblin-Davis R. Bélair G. Boivin G. and Thomas K. 2007 Bradynema listronoti n sp. (Nematoda: Allantonematidae), a parasite of the carrot weevil Listronotus oregonensis (Coleoptera: Curculionidae) in Quebec, Canada. Nematology 9608 62210.1163/156854107782024749Search in Google Scholar