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.