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.