Supplemental Material for Hoffberg et al., 2018

Figure S1: Comparison of the size distribution of library inserts in the Meraculous and HiRise assemblies.<div><br></div><div>Figure S2: The frequency of kmers at each kmer length. </div><div><br></div><div>Figure S3: The distribution of scaffold lengths in the HiRise assembly. </div><div><br></div><div>Figure S4: The cumulative percent of the assembly for a given scaffold size in the Meraculous and HiRise assemblies. </div><div><br></div><div>Table S1: A detailed list of the number of copies and percent of the assembly of transposons and repeatable elements. </div><div><br></div><p>File S1: Submission script for MAKER.</p><p><br></p> <p>File S2: MAKER executable file (maker_exe.ctl).</p><p><br></p> <p>File S3: Specifications for downstream filtering of BLAST and Exonerate alignments (maker_bopts.ctl).</p><p><br></p> <p>File S4: Primary configuration of MAKER specific options (maker_opts.ctl).</p><p><br></p> <p>File S5: Commands for training SNAP.</p> <p><br></p><p>File S6: Submission script for BLAST comparing <i>Gambusia affinis</i> with related fish.</p> <p><br></p><p>File S7: Submission script for BUSCO.</p> <p><br></p><p>File S8: Submission script for predicting ncRNAs.</p> <p><br></p><p>File S9: Illumina reads mapped to the reference in BAM format.</p><p><br></p><p>File S10: Sequence of tRNAs.</p> <p><br></p><p>File S11: Structure of tRNAs.</p> <div><br></div><div>File S12: rRNA, snRNA, snoRNA, and miRNA sequences.</div><div><br></div>