Data from: The Genome sequence of a widespread apex predator, the golden eagle (Aquila chrysaetos)

Doyle JM, Katzner TE, Bloom PH, Ji Y, Wijayawardena BK, DeWoody JA

Date Published: April 24, 2014

DOI: http://dx.doi.org/10.5061/dryad.d0md6

 

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Title annotated genes_proteins
Downloaded 507 times
Description 16,571 genes were annotated in the golden eagle genome, this fasta file describes the protein sequences (see readme.pdf for more information). Corresponding file archived in fortress is kmer70_min10000_scaffolds_revisedassembly.all.maker.proteins.
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Title annotated genes_transcripts
Downloaded 342 times
Description 16,571 genes were annotated in the golden eagle genome, this fasta files describes the transcripts (see readme.pdf for additional information). Corresponding file archived in fortress is kmer70_min10000_scaffolds_revisedassembly.all.maker.transcripts.
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Title mitochondrial genome_GE_MITObim_revised
Downloaded 12 times
Description Golden eagle mitochondrial genome sequence assembled with MITObim vs. 1.6 and MIRA MIRA 3.4.1.1.
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Title xenobiotic sequences_Golden_Eagle_BLASTN_output
Downloaded 42 times
Description blastn (DiaGrid) Input Options Query File: GoldenEagle sequences with no significant match (E<10-6) to chicken genome Database Selection: nt Custom Database Format: N Expectation Value: 1.0E-6 Word Size: 28 Search and Result Restriction Options Max Target Seqs: 1000 Output Formatting Options Format: 6 Custom Selection: qseqid sseqid qstart qend sstart send evalue bitscore pident length mismatch gapopen staxids sscinames scomnames sblastnames sskingdoms stitle
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Title transposable elements_RepeatProteinMask output_ge_v2_all
Downloaded 19 times
Description ############################ ##### RepeatProteinMask #### ############################ ## version: 4.0.2 ## command: RepeatProteinMask -noLowSimple -pvalue 1e-4 -engine abblast kmer70-v2-min200-scaffolds.fa ## output files: ge_v2_all.annot
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Title transposable elements_repeatmasker_kmer70-v2-min200-scaffolds.fa
Downloaded 10 times
Description ############################ ###### RepeatMasker ######## ############################ ## RepeatMasker version 4.0.2 ## RepeatMaskerLibrary-20130422 version ## command: RepeatMasker -nolow -no_is -norna -dir . \ -lib RepeatMaskerLib.embl.lib \ kmer70-v2-min200-scaffolds.fa ## output files: repeatmasker_kmer70-v2-min200-scaffolds.fa.masked repeatmasker_kmer70-v2-min200-scaffolds.fa.tbl
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Title transposable elements_repeatmasker_kmer70-v2-min200-scaffolds.fa
Downloaded 10 times
Description ############################ ###### RepeatMasker ######## ############################ ## RepeatMasker version 4.0.2 ## RepeatMaskerLibrary-20130422 version ## command: RepeatMasker -nolow -no_is -norna -dir . \ -lib RepeatMaskerLib.embl.lib \ kmer70-v2-min200-scaffolds.fa ## output files: repeatmasker_kmer70-v2-min200-scaffolds.fa.masked repeatmasker_kmer70-v2-min200-scaffolds.fa.tbl
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Title annotated genes_gff
Downloaded 47 times
Description 16,571 genes were annotated in the golden eagle genome, this is the .gff file associated with the annotations (see readme.pdf for additional information).
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Title transposable elements_repeatmodeler_kmer70-v2-min200-scaffolds.fa.tar
Downloaded 14 times
Description ############################ ####### RepeatModeler ###### ############################ ## version: 1.0.7 ## command: BuildDatabase -name goldenEagle_v2_tmp -engine ncbi kmer70-v2-min200-scaffolds.fa RepeatModeler -database goldenEagle_v2_tmp RepeatMasker -nolow -no_is -norna -dir . -lib Ach-v2.consensi.fa.classified kmer70-v2-min200-scaffolds.fa ## output files: Ach-v2.consensi.fa.classified repeatmodeler_kmer70-v2-min200-scaffolds.fa.masked repeatmodeler_kmer70-v2-min200-scaffolds.fa.tbl
Download README.txt (2.497 Kb)
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Title transposable elements_repeatmodeler_kmer70-v2-min200-scaffolds.fa
Downloaded 11 times
Description ############################ ####### RepeatModeler ###### ############################ ## version: 1.0.7 ## command: BuildDatabase -name goldenEagle_v2_tmp -engine ncbi kmer70-v2-min200-scaffolds.fa RepeatModeler -database goldenEagle_v2_tmp RepeatMasker -nolow -no_is -norna -dir . -lib Ach-v2.consensi.fa.classified kmer70-v2-min200-scaffolds.fa ## output files: Ach-v2.consensi.fa.classified repeatmodeler_kmer70-v2-min200-scaffolds.fa.masked repeatmodeler_kmer70-v2-min200-scaffolds.fa.tbl
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Title transposable elements_Ach-v2.consensi.fa
Downloaded 13 times
Description ############################ ####### RepeatModeler ###### ############################ ## version: 1.0.7 ## command: BuildDatabase -name goldenEagle_v2_tmp -engine ncbi kmer70-v2-min200-scaffolds.fa RepeatModeler -database goldenEagle_v2_tmp RepeatMasker -nolow -no_is -norna -dir . -lib Ach-v2.consensi.fa.classified kmer70-v2-min200-scaffolds.fa ## output files: Ach-v2.consensi.fa.classified repeatmodeler_kmer70-v2-min200-scaffolds.fa.masked repeatmodeler_kmer70-v2-min200-scaffolds.fa.tbl
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Title transposable elements_kmer70-v2-min200-scaffolds.fa.2.7.7.80.10.50.200
Downloaded 18 times
Description ############################ ########### trf ############ ############################ ## version: 4.04 ## command: trf kmer70-v2-min200-scaffolds.fa 2 7 7 80 10 50 200 -f -h ## output files: kmer70-v2-min200-scaffolds.fa.2.7.7.80.10.50.200.dat
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Title microsatellites_kmer70_min200_scaffolds_revisedassembly_allmicrosatellites.fasta
Downloaded 181 times
Description I used the MISA.pl script (http://pgrc.ipk-gatersleben.de/misa/misa.html) to identify all microsatellites present in scaffolds greater than 200 bp. Misa.pl kmer70_min200_scaffolds_revisedassembly.fasta
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Title genome assembly_kmer70_min10000_scaffolds_revisedassembly
Downloaded 18 times
Description The golden eagle genome was assembled in ABySS with the following parameters: abyss-pe s=202 n=10 k=70 l=30; followed by file specifications for 1) 'lib' -- the paired-end and mate-pair reads, 2) 'se' -- the unpaired and mate-pair reads used as single-end reads in assembly and 3) 'mp' -- the paired-end and mate-pair reads used in scaffolding.
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When using this data, please cite the original publication:

Doyle JM, Katzner TE, Bloom PH, Ji Y, Wijayawardena BK, DeWoody JA (2014) The Genome sequence of a widespread apex predator, the golden eagle (Aquila chrysaetos). PLoS ONE 9(4): e95599. http://dx.doi.org/10.1371/journal.pone.0095599

Additionally, please cite the Dryad data package:

Doyle JM, Katzner TE, Bloom PH, Ji Y, Wijayawardena BK, DeWoody JA (2014) Data from: The Genome sequence of a widespread apex predator, the golden eagle (Aquila chrysaetos). Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.d0md6
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