Data from: Long-range PCR allows sequencing of mitochondrial genomes from environmental DNA

Deiner K, Renshaw MA, Li Y, Olds BP, Lodge DM, Pfrender ME

Date Published: July 18, 2017

DOI: http://dx.doi.org/10.5061/dryad.q5gg0

 

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Title commands_used_for_analysis
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Description All commands used to execute bioinformatic pipeline.
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Title norm_50x
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Description Command used to down sample reads for de novo assembly.
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Title mitogenomes_all_corrected_reading_frame.v0301
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Description File contains the reference sequences used for mapping the .sam files to and is needed for importing .sam files into Geneious for SNP analysis
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Title JudayCreek.scaffold
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Description Contains all scaffolds that were assembled from the Juday Creek water samples.
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Title JudayCreek.scaffold.fa.blast.filter.summary.scaf
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Description List subset of scaffolds by species that were used to map to references in Geneious and is illustrated in Figure 2 of manuscript.
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Title Mesocosm_EH.scaffold
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Description Contains all scaffolds that were assembled from the even high abundance mesocosm water samples.
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Title Mesocosm_EH.scaffold.fa.blast.filter.summary.scaf
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Description List subset of scaffolds by species that were used to map to references.
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Title Mesocosm_EH.aligning.unique.sorted.MarkedDuplicates
Downloaded 2 times
Description File contains all reads mapped to references considered in study. The file in conjunction with mitogenomes_all_corrected_reading_frame.v0301.txt allows the SNPs to be called in using Geneious.
Download Mesocosm_EH.aligning.unique.sorted.Marked...es.sam (309.4 Mb)
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Title Mesocosm_SH.scaffold
Downloaded 2 times
Description Contains all scaffolds that were assembled from the skewed high abundance mesocosm water samples.
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Title Mesocosm_SH.scaffold.fa.blast.filter.summary.scaf
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Description List subset of scaffolds by species that were used to map to references.
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Title Mesocosm_SH.aligning.unique.sorted.MarkedDuplicates
Downloaded 2 times
Description File contains all reads mapped to references considered in study. The file in conjunction with mitogenomes_all_corrected_reading_frame.v0301.txt allows the SNPs to be called in using Geneious.
Download Mesocosm_SH.aligning.unique.sorted.Marked...es.sam (313.9 Mb)
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Title Mock.50x.scaffold
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Description Contains all scaffolds that were assembled from the mock community sample.
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Title Mock.50x.scaffold.fa.blast.filter.summary.scaf
Downloaded 2 times
Description List subset of scaffolds by species that were used to map to references.
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Title Mock.aligning.unique.sorted.MarkedDuplicates.sam
Downloaded 2 times
Description File contains all reads mapped to references considered in study. The file in conjunction with mitogenomes_all_corrected_reading_frame.v0301.txt allows the SNPs to be called in using Geneious.
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Title JudayCreek.aligning.unique.sorted.MarkedDuplicates
Downloaded 5 times
Description Zipped file contains all reads mapped to references considered in study. The file in conjunction with mitogenomes_all_corrected_reading_frame.v0301.txt allows the SNPs to be called in using Geneious and for generation of mapping results illustrated in Figure 2.
Download JudayCreek.aligning.unique.sorted.MarkedD...am.zip (1.217 Gb)
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When using this data, please cite the original publication:

Deiner K, Renshaw MA, Li Y, Olds BP, Lodge DM, Pfrender ME (2017) Long-range PCR allows sequencing of mitochondrial genomes from environmental DNA. Methods in Ecology and Evolution, online in advance of print. http://dx.doi.org/10.1111/2041-210x.12836

Additionally, please cite the Dryad data package:

Deiner K, Renshaw MA, Li Y, Olds BP, Lodge DM, Pfrender ME (2017) Data from: Long-range PCR allows sequencing of mitochondrial genomes from environmental DNA. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.q5gg0
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