Draft de novo genome assemblies of a male and female Amphibolurus muricatus (jacky dragon)

• AmpMurF_1.0.fa.tar.gz: de novo nuclear genome assembly of a female <em>A. muricatus</em><br> • AmpMurM_1.0.fa.tar.gz: de novo nuclear genome assembly of a male <em>A. muricatus </em> <strong>Methods</strong> Raw 10X data were assembled with Supernova v2.1.1 (Weisenfeld et al. 2017) and a FASTA file was generated using the ‘pseudohap style’ option in Supernova mkoutput. All female (~450 M) and male (~550 M) <em>A. muricatus</em> read pairs were utilized (female sequencing depth ~50.3; male, ~47.8×). The resulting assembly was further scaffolded with ARKS v1.0.3 (Coombe et al. 2018), reusing the 10X reads, and the companion LINKS program (v1.8.7) (Warren et al. 2015). ARKS employs a k-mer approach to map linked barcodes to the contigs in the initial Supernova assembly to generate a scaffold graph with estimated distances for LINKS input. Next, RNA-seq reads (from brain, ovary, and testis; see below) were filtered (i.e., 'cleaned') to remove adapters and low-quality reads using Flexbar v3.4.0 (Roehr et al. 2017; Dodt et al. 2012) and used to further re-scaffold the assembly with P_RNA_scaffolder (Zhu et al. 2018). The default Flexbar settings discards all reads with any uncalled bases. A final round of scaffolding was performed on the resulting assembly using L_RNA_scaffolder (Xue et al. 2013). We used GapCloser v1.12 (part of SOAPdenovo2) (Luo et al. 2012) to fill gaps in the assembly. GapCloser was run using the parameter ‘-l 150’) and ‘clean’ 10X Genomics reads PE reads. <strong>References</strong> Coombe, L., J. Zhang, B.P. Vandervalk, J. Chu, S.D. Jackman et al., 2018 ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers. BMC Bioinformatics 19 (1):234. Dodt, M., J.T. Roehr, R. Ahmed, and C. Dieterich, 2012 FLEXBAR-Flexible Barcode and Adapter Processing for Next-Generation Sequencing Platforms. Biology (Basel) 1 (3):895-905. Luo, R., B. Liu, Y. Xie, Z. Li, W. Huang et al., 2012 SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 1 (1):18. Roehr, J.T., C. Dieterich, and K. Reinert, 2017 Flexbar 3.0 - SIMD and multicore parallelization. Bioinformatics 33 (18):2941-2942. Warren, R.L., C. Yang, B.P. Vandervalk, B. Behsaz, A. Lagman et al., 2015 LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads. Gigascience 4:35. Weisenfeld, N.I., V. Kumar, P. Shah, D.M. Church, and D.B. Jaffe, 2017 Direct determination of diploid genome sequences. Genome Res 27 (5):757-767. Xue, W., J.T. Li, Y.P. Zhu, G.Y. Hou, X.F. Kong et al., 2013 L_RNA_scaffolder: scaffolding genomes with transcripts. BMC Genomics 14:604. Zhu, B.H., J. Xiao, W. Xue, G.C. Xu, M.Y. Sun et al., 2018 P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads. BMC Genomics 19 (1):175.