README
File Archive for Nowak et al. (Molecular Ecology Resources)

Dniv87_Chicago_SSPACE_LINKS14_1kb_ChromonomerRun4_integrated_20July2018.fasta -  The Draba nivalis genome assembly. Note that the chromosome naming in this file follows the "old" format (lg1 - lg8), but in the manuscript, these have been renamed according to the following translation table:
OLD		NEW	
lg1		Dniv7
lg2		Dniv8
lg3		Dniv2
lg4		Dniv3
lg5		Dniv1
lg6		Dniv4
lg7		Dniv6
lg8		Dniv5

Draba_TE_annotation_March2019.gff3 - Annotation of repetitive elements in the Draba nivalis genome.

LTR_Helitron_TIR_SINE_LINE_new_helitron_filter_uniq.fasta - Repeat library produced for the annotation of repetitive elements.

DN87_whole_26Jan17_Trinity_topISO.fasta.transdecoder.cds -  De novo transcriptome assembly of Draba nivalis generated using RNAseq data from leaves, roots, flower buds, and mature flowers. Raw data available on GenBank.

Dniva.Maker.Run5.all.proteins.NumberedGenes.fasta - The translated amino acid sequences of all 33557 transcripts annotated in the Draba nivalis genome assembly. Transcripts are numbered, such that the transcript names are equivalent to those found in the supplementary tables of the manuscript.

Dniva.Maker.Run5.all.transcripts.NumberedGenes.fasta - The coding sequences of all 33557 transcripts annotated in the Draba nivalis genome assembly. Transcripts are numbered, such that the transcript names are equivalent to those found in the supplementary tables of the manuscript.

Dniv87_Chicago_SSPACE_LINKS14_1kb_ChromonomerRun4_integrated_20July2018_unwrap.all.maker.transcripts.Run5.fasta - The same file as Dniva.Maker.Run5.all.transcripts.NumberedGenes.fasta, but with the default transcript names provided by Maker.

Dniv87_Chicago_SSPACE_LINKS14_1kb_ChromonomerRun4_integrated_20July2018_unwrap.all.Run5.maker.genes.gff - The annotation of genes produced by Maker, note that the naming of genes follows the transcript file Dniv87_Chicago_SSPACE_LINKS14_1kb_ChromonomerRun4_integrated_20July2018_unwrap.all.maker.transcripts.Run5.fasta.

species_joint_variants_rmind_95_8DP200_Q50_bisnps.vcf - VCF file of ddRAD genotypes for all F2 individuals genotyped to produce the genetic map used in the final chromosome-scale scaffolding of the Draba nivalis genome. 

4 files: Lane1_1-48.tar.gz, Lane1_49-96.tar.gz, Lane1_97-144.tar.gz, Lane1_145-192.tar.gz - Demultiplexed Fastq files containing all of the ddRAD sequencing data for each of 96 F2 individuals run in a single Illumina HiSeq 2500 lane

4 files: Lane2_1-48.tar.gz, Lane2_49-96.tar.gz, Lane2_97-144.tar.gz, Lane2_145-192.tar.gz, - Demultiplexed Fastq files containing all of the ddRAD sequencing data for each of 96 F2 individuals run in a single Illumina HiSeq 2500 lane

4 files: Lane3_1-48.tar.gz, Lane3_49-96.tar.gz, Lane3_97-144.tar.gz, Lane3_145-192.tar.gz - Demultiplexed Fastq files containing all of the ddRAD sequencing data for each of 96 F2 individuals run in a single Illumina HiSeq 2500 lane

4 files: Lane4_1-48.tar.gz, Lane4_49-96.tar.gz, Lane4_97-144.tar.gz, Lane4_145-192.tar.gz - Demultiplexed Fastq files containing all of the ddRAD sequencing data for each of 96 F2 individuals run in a single Illumina HiSeq 2500 lane

4 files: Lane5_1-48.tar.gz, Lane5_49-96.tar.gz, Lane5_97-144.tar.gz Lane5_145-192.tar.gz - Demultiplexed Fastq files containing all of the ddRAD sequencing data for each of 96 F2 individuals run in a single Illumina HiSeq 2500 lane

4 files: Lane6_1-48.tar.gz, Lane6_49-96.tar.gz, Lane6_97-144.tar.gz, Lane6_145-192.tar.gz - Demultiplexed Fastq files containing all of the ddRAD sequencing data for each of 96 F2 individuals run in a single Illumina HiSeq 2500 lane