17 files

Supplemental Material for Hoffberg et al., 2018

posted on 26.04.2018 by Sandra L. Hoffberg, Nicholas J. Troendle, Travis C. Glenn, Ousman Mahmud, Swarnali Louha, Domitille Chalopin, Jeffrey L. Bennetzen, Rodney Mauricio
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.


Article title

A High-Quality Reference Genome for the Invasive Mosquitofish Gambusia affinis Using a Chicago Library

Manuscript #


Article DOI