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Supplemental Material for Hoffberg et al., 2018

posted on 2018-04-26, 20:34 authored 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

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