Supplemental Material for Hoffberg et al., 2018
Sandra L. Hoffberg
Nicholas J. Troendle
Travis C. Glenn
Ousman Mahmud
Swarnali Louha
Domitille Chalopin
Jeffrey L. Bennetzen
Rodney Mauricio
10.25387/g3.6157706.v1
https://gsajournals.figshare.com/articles/dataset/Supplemental_Material_for_Hoffberg_et_al_2018/6157706
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>
2018-04-26 20:34:16
Gambusia affinis
Dovetail Genomics
MAKER
SNAP
BLAST
BUSCO
ncRNA
tRNA
Poecilid
whole genome sequencing
de novo assembly
HiRise
Genomics