Supplemental Material for Hoffberg et al., 2018

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