Data from: Major improvements to the Heliconius melpomene genome assembly used to confirm 10 chromosome fusion events in 6 million years of butterfly evolution

Davey JW, Chouteau M, Barker SL, Maroja L, Baxter SW, Simpson F, Joron M, Mallet J, Dasmahapatra KK, Jiggins CD

Date Published: January 21, 2016

DOI: http://dx.doi.org/10.5061/dryad.3s795

 

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Title Eueides.Hmel2.vcf.gz
Downloaded 8 times
Description Variant calls for Eueides isabella cross aligned to Hmel2.fa
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Title GitHub.tar.gz
Downloaded 7 times
Description A snapshot of the bespoke code written to reassemble the genome, available from https://github.com/johnomics/Heliconius_melpomene_version_2, commit f826fd1 from Dec 10, 2015
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Title Genome.tar.gz
Downloaded 7 times
Description A snapshot of the Hmel2 distribution available from butterflygenome.org
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Title Hmel_cross.Hmel_haplotype_scaffolds.vcf.gz
Downloaded 7 times
Description Variant calls for Heliconius melpomene mapping cross aligned to Hmel1-1 haplotype scaffolds (Hmel_haplotype_scaffolds.fas)
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Title Hmel_cross.Hmel1-1_primaryScaffolds.vcf.gz
Downloaded 7 times
Description Variant calls for Heliconius melpomene mapping cross aligned to Hmel1-1 primary scaffolds (Hmel1-1_primaryScaffolds.fa)
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Title Hmel_cross.linkage_map.clean.db.gz
Downloaded 13 times
Description SQLite3 database containing scaffold_map and chromosome_map tables used to reassemble genome, fixing all identified linkage errors, recalculating cM values and reversing chromosomes where necessary
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Title Hmel_cross.linkage_map.db.gz
Downloaded 12 times
Description SQLite3 database containing marker information for linkage map (see README.txt for table descriptions)
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Title Hmel1-1_haploid.fa.gz
Downloaded 6 times
Description Hmel1-2 genome collapsed by HaploMerger
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Title Hmel1-2_pacbio_merge.fa.gz
Downloaded 3 times
Description Hmel1-2_haploid and pacbio_haploid merged by HaploMerger
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Title Hmel1-2.fa.gz
Downloaded 8 times
Description Hmel1-1 genome updated to correct all identified misassemblies
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Title pacbio_falcon_assembly.fa.gz
Downloaded 3 times
Description Initial assembly of PacBio reads with FALCON
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Title pacbio_haploid.fa.gz
Downloaded 7 times
Description FALCON PacBio assembly collapsed by HaploMerger
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Title readdepth_gc_1kb_windows.Hmel2.adjusted.tsv.gz
Downloaded 4 times
Description GC content and median read depths unadjusted and adjusted for GC content in 1kb windows for F1 father
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Title README
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When using this data, please cite the original publication:

Davey JW, Chouteau M, Barker SL, Maroja L, Baxter SW, Simpson F, Joron M, Mallet J, Dasmahapatra KK, Jiggins CD (2016) Major improvements to the Heliconius melpomene genome assembly used to confirm 10 chromosome fusion events in 6 million years of butterfly evolution. G3: Genes - Genomes - Genetics 6(3): 695-708. http://dx.doi.org/10.1534/g3.115.023655

Additionally, please cite the Dryad data package:

Davey JW, Chouteau M, Barker SL, Maroja L, Baxter SW, Simpson F, Joron M, Mallet J, Dasmahapatra KK, Jiggins CD (2016) Data from: Major improvements to the Heliconius melpomene genome assembly used to confirm 10 chromosome fusion events in 6 million years of butterfly evolution. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.3s795
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