The data for: Genomic resources and draft reference assemblies of the human and porcine scabies mites, Sarcoptes scabiei var. hominis and var. suis

Dataset type: Genomic
Data released on May 20, 2016

Mofiz E; Holt D; Seemann T; Currie BJ; Fischer K; Papenfuss AT (2016): The data for: Genomic resources and draft reference assemblies of the human and porcine scabies mites, Sarcoptes scabiei var. hominis and var. suis GigaScience Database. http://dx.doi.org/10.5524/100198

DOI10.5524/100198

The scabies mite, Sarcoptes scabiei, is a parasitic arachnid and cause of the infectious skin disease scabies in humans or mange in many animal species. We sequenced the genome of two samples of S. scabiei var. hominis obtained from unrelated patients with crusted scabies located in different parts of northern Australia using the Illumina HiSeq. We also sequenced samples of S. scabiei var. suis from a pig model. Due to the small size of scabies mite, these data are derived from pools of thousands of mites and are metagenomic, including host and microbiome DNA. We performed cleaning and de novo assembly and present Sarcoptes scabiei var. hominis and var. suis draft reference genomes. We have constructed a preliminary annotation of this reference comprising 13,226 putative coding sequences based on sequence similarity to known proteins.

Additional details

Read the peer-reviewed publication(s):

Mofiz, E., Holt, D. C., Seemann, T., Currie, B. J., Fischer, K., & Papenfuss, A. T. (2016). Genomic resources and draft assemblies of the human and porcine varieties of scabies mites, Sarcoptes scabiei var. hominis and var. suis. GigaScience, 5(1). doi:10.1186/s13742-016-0129-2

Accessions (data included in GigaDB):

BioProject: PRJEB12428

Accessions (data not in GigaDB):

ENA: LN874268
ENA: LN874269
ENA: LN874270





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Sarcoptes scabiei var. hominis patient A52283  Sarcoptes scabiei Alternative accession-SRA Sample:ERS1037125
Alternative accession-BioSample:SAMEA3729976
Infra specific name:hominis
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Sarcoptes scabiei var. hominis patient B52283  Sarcoptes scabiei Alternative accession-SRA Sample:ERS1037126
Alternative accession-BioSample:SAMEA3729977
Infra specific name:hominis
...
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Sarcoptes scabiei var suis pig unwashed52283  Sarcoptes scabiei Alternative accession-SRA Sample:ERS1037205
Alternative accession-BioSample:SAMEA3730056
Infra specific name:suis
...
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Sarcoptes scabiei var suis pig washed 152283  Sarcoptes scabiei Alternative accession-SRA Sample:ERS1037206
Alternative accession-BioSample:SAMEA3730057
Infra specific name:suis
...
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Sarcoptes scabiei var suis pig washed 252283  Sarcoptes scabiei Alternative accession-SRA Sample:ERS1037207
Alternative accession-BioSample:SAMEA3730058
Infra specific name:suis
...
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Sarcoptes scabiei var suis pig washed 352283  Sarcoptes scabiei Alternative accession-SRA Sample:ERS1037208
Alternative accession-BioSample:SAMEA3730059
Infra specific name:suis
...
+
Displaying 1-6 of 6 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
Sarcoptes scabiei var. hominis patient AAssemblyFASTA55.03 MB2016-04-20
AssemblyFASTA52.01 MB2016-04-20
AssemblyFASTA61.17 MB2016-04-20
AssemblyFASTA46.13 MB2016-04-20
AssemblyFASTA50.7 MB2016-04-20
AssemblyFASTA51.82 MB2016-04-20
Sarcoptes scabiei var suis pig unwashedGenome assemblyFASTA55.33 MB2016-04-20
Sarcoptes scabiei var suis pig washed 1Genome assemblyFASTA69.61 MB2016-04-20
Sarcoptes scabiei var suis pig washed 2Genome assemblyFASTA63.42 MB2016-04-20
Sarcoptes scabiei var suis pig washed 3Genome assemblyFASTA55.03 MB2016-04-20
Displaying 1-10 of 14 File(s).

Protocols.io:

Date Action
May 31, 2016 preliminary_platanus_assembly_pig_washed3.fa: additional file attribute added
May 31, 2016 File patient_A_major_scaffold_assembly.fa updated
May 20, 2016 Dataset publish
May 31, 2016 File patient_A_major_scaffold_assembly.fa updated
May 31, 2016 Additional file preliminary_platanus_assembly_pig_unwashed.fa added
May 31, 2016 preliminary_platanus_assembly_pig_unwashed.fa: additional file attribute added
May 31, 2016 preliminary_platanus_assembly_pig_unwashed.fa: additional file attribute added
May 31, 2016 Additional file preliminary_platanus_assembly_pig_washed1.fa added
May 31, 2016 preliminary_platanus_assembly_pig_washed1.fa: additional file attribute added
May 31, 2016 preliminary_platanus_assembly_pig_washed1.fa: additional file attribute added
May 31, 2016 Additional file preliminary_platanus_assembly_pig_washed2.fa added
May 31, 2016 preliminary_platanus_assembly_pig_washed2.fa: additional file attribute added
May 31, 2016 preliminary_platanus_assembly_pig_washed2.fa: additional file attribute added
May 31, 2016 Additional file preliminary_platanus_assembly_pig_washed3.fa added
May 31, 2016 preliminary_platanus_assembly_pig_washed3.fa: additional file attribute added
May 31, 2016 File patient_A_major_scaffold_assembly.fa updated
May 31, 2016 File patient_A_major_scaffold_assembly.fa updated
May 31, 2016 File patient_A_major_scaffold_assembly.fa updated
May 31, 2016 File patient_A_major_scaffold_assembly.fa updated
May 31, 2016 File patient_A_major_scaffold_assembly.fa updated
May 31, 2016 File patient_A_major_scaffold_assembly.fa updated
May 31, 2016 File patient_A_major_scaffold_assembly.fa updated
June 3, 2016 Manuscript Link updated : 10.1186/s13742-016-0129-2