%0 Generic %A Hoffberg, Sandra L. %A Troendle, Nicholas J. %A C. Glenn, Travis %A Mahmud, Ousman %A Louha, Swarnali %A Chalopin, Domitille %A L. Bennetzen, Jeffrey %A Mauricio, Rodney %D 2018 %T Supplemental Material for Hoffberg et al., 2018 %U https://gsajournals.figshare.com/articles/dataset/Supplemental_Material_for_Hoffberg_et_al_2018/6157706 %R 10.25387/g3.6157706.v1 %2 https://ndownloader.figshare.com/files/11216879 %2 https://ndownloader.figshare.com/files/11216882 %2 https://ndownloader.figshare.com/files/11212205 %2 https://ndownloader.figshare.com/files/11212181 %2 https://ndownloader.figshare.com/files/11212190 %2 https://ndownloader.figshare.com/files/11212184 %2 https://ndownloader.figshare.com/files/11212193 %2 https://ndownloader.figshare.com/files/11212196 %2 https://ndownloader.figshare.com/files/11212199 %2 https://ndownloader.figshare.com/files/11212202 %2 https://ndownloader.figshare.com/files/11212208 %2 https://ndownloader.figshare.com/files/11212214 %2 https://ndownloader.figshare.com/files/11212211 %2 https://ndownloader.figshare.com/files/11212217 %2 https://ndownloader.figshare.com/files/11213357 %2 https://ndownloader.figshare.com/files/11212220 %2 https://ndownloader.figshare.com/files/11212226 %K Gambusia affinis %K Dovetail Genomics %K MAKER %K SNAP %K BLAST %K BUSCO %K ncRNA %K tRNA %K Poecilid %K whole genome sequencing %K de novo assembly %K HiRise %K Genomics %X 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.

%I GSA Journals