Data from: "Complete mitochondrial and partial nuclear genomes for the jack species Caranx ignobilis (Forsskål, 1775) and C. melampygus (Cuvier, 1833) (Perciformes:Carangidae) from the High Hawaiian Islands" in Genomic Resources Notes accepted 1 October 2013 – 30 November 2013

 

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Title Car_ign_all_nucleotide_contigs_from_Ray_assembly
Downloaded 8 times
Description FASTA file of all nucleotide contigs assembled from 139,329,276 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx ignobilis
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Title Car_ign_only_1200bp+_nucleotide_contigs_from_Ray_assembly
Downloaded 6 times
Description FASTA file of only nucleotide contigs >=1,200 bp assembled from 139,329,276 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx ignobilis
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Title Car_mel_all_nucleotide_contigs_from_Ray_assembly
Downloaded 7 times
Description FASTA file of all nucleotide contigs assembled from 133,681,136 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx melampygus
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Title Car_mel_only_1200bp+_nucleotide_contigs_from_Ray_assembly
Downloaded 4 times
Description FASTA file of only nucleotide contigs >=1,200 bp assembled from 133,681,136 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx melampygus
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Title Car_ign_all_100+amino_acids_ORFs_from_1200bp+_contigs
Downloaded 5 times
Description FASTA file of all potential open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=1,200 bp assembled from 139,329,276 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx ignobilis
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Title Car_ign_all_100+amino_acids_ORFs_from_1200bp+_contigs_to_Danio.parsed
Downloaded 8 times
Description Parsed BLAST output of all potential open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=1,200 bp assembled from 139,329,276 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx ignobilis. Subject database (DB) was the protein list from the fully sequenced genome of Danio available from NCBI.
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Title Car_ign_100+amino_acids_ORFs_from_1200bp+_contigs_to_Danio.parsed.filtered
Downloaded 7 times
Description Parsed BLAST output of all potential open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=1,200 bp assembled from 139,329,276 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx ignobilis. Subject database (DB) was the protein list from the fully sequenced genome of Danio available from NCBI. This file is filtered to only contain hits with bit scores. >=80.
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Title Car_ign_100+amino_acids_ORFs_from_1200bp+_contigs_to_Danio_all_hits
Downloaded 4 times
Description Gene list of all hit descriptors for potential open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=1,200 bp assembled from 139,329,276 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx ignobilis. Subject database (DB) was the protein list from the fully sequenced genome of Danio available from NCBI. This file is filtered to only contain hits with bit scores >=80.
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Title Car_ign_100+amino_acids_ORFs_from_1200bp+_contigs_to_Danio_unique_hits
Downloaded 5 times
Description Gene list of only unique hit descriptors for potential open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=1,200 bp assembled from 139,329,276 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx ignobilis. Subject database (DB) was the protein list from the fully sequenced genome of Danio available from NCBI. This file is filtered to only contain hits with bit scores >=80.
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Title Car_ign_100+amino_acids_ORFs_from_1200bp+_contigs_to_Danio_all_vs_unique_hits.diff
Downloaded 4 times
Description Difference file between complete gene list and only unique hit descriptors for potential open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=1,200 bp assembled from 139,329,276 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx ignobilis. Subject database (DB) was the protein list from the fully sequenced genome of Danio available from NCBI. This file is filtered to only contain hits with bit scores >=80.
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Title Car_ign_100+amino_acids_ORFs_from_1200bp+_contigs_to_Danio_as_aa
Downloaded 2 times
Description FASTA file of open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=1,200 bp assembled from 139,329,276 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx ignobilis. Subject database (DB) was the protein list from the fully sequenced genome of Danio available from NCBI. This file is filtered to only contain hits with bit scores >=80.
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Title Car_ign_all_100+amino_acids_ORFs_from_1200bp+_contigs_to_Takifugu.parsed
Downloaded 7 times
Description Parsed BLAST output of all potential open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=1,200 bp assembled from 139,329,276 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx ignobilis. Subject database (DB) was the protein list from the fully sequenced genome of Takifugu available from NCBI.
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Title Car_ign_100+amino_acids_ORFs_from_1200bp+_contigs_to_Takifugu.parsed.filtered
Downloaded 5 times
Description Parsed BLAST output of all potential open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=1,200 bp assembled from 139,329,276 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx ignobilis. Subject database (DB) was the protein list from the fully sequenced genome of Takifugu available from NCBI. This file is filtered to only contain hits with bit scores >=80.
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Title Car_ign_100+amino_acids_ORFs_from_1200bp+_contigs_to_Takifugu_all_hits
Downloaded 6 times
Description Gene list of all hit descriptors for potential open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=1,200 bp assembled from 139,329,276 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx ignobilis. Subject database (DB) was the protein list from the fully sequenced genome of Takifugu available from NCBI. This file is filtered to only contain hits with bit scores >=80.
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Title Car_ign_100+amino_acids_ORFs_from_1200bp+_contigs_to_Takifugu_unique_hits
Downloaded 6 times
Description Gene list of only unique hit descriptors for potential open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=1,200 bp assembled from 139,329,276 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx ignobilis. Subject database (DB) was the protein list from the fully sequenced genome of Takifugu available from NCBI. This file is filtered to only contain hits with bit scores >=80.
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Title Car_ign_100+amino_acids_ORFs_from_1200bp+_contigs_to_Takifugu_all_vs_unique_hits.diff
Downloaded 4 times
Description Difference file between complete gene list and only unique hit descriptors for potential open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=1,200 bp assembled from 139,329,276 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx ignobilis. Subject database (DB) was the protein list from the fully sequenced genome of Takifugu available from NCBI. This file is filtered to only contain hits with bit scores >=80.
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Title Car_ign_100+amino_acids_ORFs_from_1200bp+_contigs_to_Takifugu_as_aa
Downloaded 8 times
Description FASTA file of open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=1,200 bp assembled from 139,329,276 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx ignobilis. Subject database (DB) was the protein list from the fully sequenced genome of Takifugu available from NCBI. This file is filtered to only contain hits with bit scores >=80.
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Title Car_mel_all_100+amino_acids_ORFs_from_1200bp+_contigs
Downloaded 9 times
Description FASTA file of all potential open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=1,200 bp assembled from 133,681,136 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx melampygus
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Title Car_mel_all_100+amino_acids_ORFs_from_1200bp+_contigs_to_Danio.parsed
Downloaded 3 times
Description Parsed BLAST output of all potential open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=1,200 bp assembled from 133,681,136 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx melampygus. Subject database (DB) was the protein list from the fully sequenced genome of Danio available from NCBI.
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Title Car_mel_100+amino_acids_ORFs_from_1200bp+_contigs_to_Danio.parsed.filtered
Downloaded 2 times
Description Parsed BLAST output of all potential open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=1,200 bp assembled from 133,681,136 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx melampygus. Subject database (DB) was the protein list from the fully sequenced genome of Danio available from NCBI. This file is filtered to only contain hits with bit scores >=80.
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Title Car_mel_100+amino_acids_ORFs_from_1200bp+_contigs_to_Danio_all_hits
Downloaded 4 times
Description Gene list of all hit descriptors for potential open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=1,200 bp assembled from 133,681,136 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx melampygus. Subject database (DB) was the protein list from the fully sequenced genome of Danio available from NCBI. This file is filtered to only contain hits with bit scores >=80.
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Title Car_mel_100+amino_acids_ORFs_from_1200bp+_contigs_to_Danio_unique_hits
Downloaded 8 times
Description Gene list of only unique hit descriptors for potential open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=1,200 bp assembled from 133,681,136 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx melampygus. Subject database (DB) was the protein list from the fully sequenced genome of Danio available from NCBI. This file is filtered to only contain hits with bit scores >=80.
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Title Car_mel_100+amino_acids_ORFs_from_1200bp+_contigs_to_Danio_all_vs_unique_hits.diff
Downloaded 6 times
Description Difference file between complete gene list and only unique hit descriptors for potential open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=1,200 bp assembled from 133,681,136 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx melampygus. Subject database (DB) was the protein list from the fully sequenced genome of Danio available from NCBI. This file is filtered to only contain hits with bit scores >=80.
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Title Car_mel_100+amino_acids_ORFs_from_1200bp+_contigs_to_Danio_as_aa
Downloaded 3 times
Description FASTA file of open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=1,200 bp assembled from 133,681,136 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx melampygus. Subject database (DB) was the protein list from the fully sequenced genome of Danio available from NCBI. This file is filtered to only contain hits with bit scores >=80.
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Title Car_mel_all_100+amino_acids_ORFs_from_1200bp+_contigs_to_Takifugu.parsed
Downloaded 5 times
Description Parsed BLAST output of all potential open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=1,200 bp assembled from 133,681,136 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx melampygus. Subject database (DB) was the protein list from the fully sequenced genome of Takifugu available from NCBI.
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Title Car_mel_100+amino_acids_ORFs_from_1200bp+_contigs_to_Takifugu.parsed.filtered
Downloaded 8 times
Description Parsed BLAST output of all potential open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=1,200 bp assembled from 133,681,136 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx melampygus. Subject database (DB) was the protein list from the fully sequenced genome of Takifugu available from NCBI. This file is filtered to only contain hits with bit scores >=80.
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Title Car_mel_100+amino_acids_ORFs_from_1200bp+_contigs_to_Takifugu_all_hits
Downloaded 10 times
Description Gene list of all hit descriptors for potential open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=1,200 bp assembled from 133,681,136 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx melampygus. Subject database (DB) was the protein list from the fully sequenced genome of Takifugu available from NCBI. This file is filtered to only contain hits with bit scores >=80.
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Title Car_mel_100+amino_acids_ORFs_from_1200bp+_contigs_to_Takifugu_unique_hits
Downloaded 4 times
Description Gene list of only unique hit descriptors for potential open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=1,200 bp assembled from 133,681,136 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx melampygus. Subject database (DB) was the protein list from the fully sequenced genome of Takifugu available from NCBI. This file is filtered to only contain hits with bit scores >=80.
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Title Car_mel_100+amino_acids_ORFs_from_1200bp+_contigs_to_Takifugu_all_vs_unique_hits.diff
Downloaded 8 times
Description Difference file between complete gene list and only unique hit descriptors for potential open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=1,200 bp assembled from 133,681,136 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx melampygus. Subject database (DB) was the protein list from the fully sequenced genome of Takifugu available from NCBI. This file is filtered to only contain hits with bit scores >=80.
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Title Car_mel_100+amino_acids_ORFs_from_1200bp+_contigs_to_Takifugu_as_aa
Downloaded 4 times
Description FASTA file of open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=1,200 bp assembled from 133,681,136 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx melampygus. Subject database (DB) was the protein list from the fully sequenced genome of Takifugu available from NCBI. This file is filtered to only contain hits with bit scores >=80.
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Title Car_ign_all_intragenomic_SNP_indel_variation_from_1200bp+_contigs
Downloaded 4 times
Description Variant call format (VCF) file containing potential single nucleotide polymorphisms (SNPs) and indels variation extracted from nucleotide contigs >=1,200 bp assembled from 139,329,276 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx ignobilis. The following filters were applied with the program vcf-annotate: –f +/c3,10/Q=20/d=15/D=25. This file contains SNPs and indels that DID and DID NOT pass filtering.
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Title Car_ign_intragenomic_SNP_indel_variation_from_1200bp+_contigs.filtered
Downloaded 9 times
Description Variant call format (VCF) file containing potential single nucleotide polymorphisms (SNPs) and indels variation extracted from nucleotide contigs >=1,200 bp assembled from 139,329,276 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx ignobilis. The following filters were applied with the program vcf-annotate: –f +/c3,10/Q=20/d=15/D=25. This file contains ONLY SNPs and indels that DID pass filtering.
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Title Car_mel_all_intragenomic_SNP_indel_variation_from_1200bp+_contigs
Downloaded 6 times
Description Variant call format (VCF) file containing potential single nucleotide polymorphisms (SNPs) and indels variation extracted from nucleotide contigs >=1,200 bp assembled from 133,681,136 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx melampygus. The following filters were applied with the program vcf-annotate: –f +/c3,10/Q=20/d=15/D=25. This file contain SNPs and indels that DID and DID NOT pass filtering.
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Title Car_mel_intragenomic_SNP_indel_variation_from_1200bp+_contigs.filtered
Downloaded 7 times
Description Variant call format (VCF) file containing potential single nucleotide polymorphisms (SNPs) and indels variation extracted from nucleotide contigs >=1,200 bp assembled from 133,681,136 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx melampygus. The following filters were applied with the program vcf-annotate: –f +/c3,10/Q=20/d=15/D=25. This file contains ONLY SNPs and indels that DID pass filtering.
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When using this data, please cite the original publication:

Genomic Resources Development Consortium, Keller SR, Nelson, DM, Pylant C, Santos SR, Trott R (2014) Genomic Resources Notes accepted 1 October 2013 – 30 November 2013. Molecular Ecology Resources 14(2): 435–436. http://dx.doi.org/10.1111/1755-0998.12221

Additionally, please cite the Dryad data package:

Santos SR (2013) Data from: "Complete mitochondrial and partial nuclear genomes for the jack species Caranx ignobilis (Forsskål, 1775) and C. melampygus (Cuvier, 1833) (Perciformes:Carangidae) from the High Hawaiian Islands" in Genomic Resources Notes accepted 1 October 2013 – 30 November 2013. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.6gr7t
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