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Sample data
Together with the script, we provide the ZIP archive (1.8 GB) that contains exemplary input files for running the script: Oxalis genome skim data and transcriptome as well as the Ricinus cpDNA and mtDNA reference sequences. For generation of the genome skim data see Schmickl et al. (2016).
The package contains
- input1_JHCN_Oxalis_corniculata_transcriptome_data.fa - Oxalis corniculata transcriptome (parameter
-f). - input2_Ricinus_communis_reference_plastid_genome.fsa - cpDNA reference (parameter
-c), GenBank reference number NC_016736. - input3_J12_Oxalis_obtusa_J12_genome_skim_data_R1.fastq - paired-end genome skim data, file 1 (parameter
-t). - input4_J12_Oxalis_obtusa_J12_genome_skim_data_R2.fastq - paired-end genome skim data, file 2 (parameter
-q). - input5_Ricinus_communis_reference_mitochondrial_genome.fasta - mtDNA reference (parameter
-m), GenBank reference number NC_015141.
The transcriptome input file is unpublished data from G. K.-S. Wong et al. Data can be also found under
- http://www.onekp.com/ (Information about 1kP project)
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http://www.onekp.com/samples/list.php (Search for
JHCN) - http://www.onekp.com/samples/single.php?id=JHCN
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http://www.onekp.com/public_data.html (Search for
JHCNand downloadJHCN-SOAPdenovo-Trans-assembly.fa.bz2)
The transcriptome FASTA file used for the probe design is named JHCN-SOAPdenovo-Trans-assembly.dnas.out and can be found under JHCN/Assembly/JHCN-SOAPdenovo-Trans-translated/.
Information about how to get access to data download is given in Matasci N, Hung L-H, Yan Z, Carpenter EJ, Wickett NJ, Mirarab S, Nguyen N, Warnow T, Ayyampalayam S, Barker M, Burleigh JG, Gitzendanner MA, Wafula E, Der JP, dePamphilis CW, Roure B, Philippe H, Ruhfel BR, Miles NW, Graham SW, Mathews S, Surek B, Melkonian M, Soltis DE, Soltis PS, Rothfels C, Pokorny L, Shaw JA, DeGironimo L, Stevenson DW, Villarreal JC, Chen T, Kutchan TM, Rolf M, Baucom RS, Deyholos MK, Samudrala R, Tian Z, Wu X, Sun X, Zhang Y, Wang J, Leebens-Mack J and Wong G K-S (2014) Data access for the 1,000 Plants (1KP) project. GigaScience 3:17.
See README and PDF manual for explanation of command line parameters.
Download from https://github.com/V-Z/sondovac/releases/tag/sample-data-2.0
Sondovač is a script to create orthologous low-copy nuclear probes from transcriptome and genome skim data for target enrichment. When using Sondovač, please, cite Schmickl et al 2016. Wiki home.