Data from: High-throughput amplicon sequencing of rRNA genes requires a copy number correction to accurately reflect the effects of management practices on soil nematode community structure

Darby BJ, Todd TC, Herman MA

Date Published: August 1, 2013

DOI: http://dx.doi.org/10.5061/dryad.t8g16

 

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Title Sequence-based data
Downloaded 6 times
Description This comma-delimited file contains the raw number of sequences for each of 131 "species" (Genbank accessions) for 64 field samples (16 plots x 2 seasons x 2 reps) and two "test" samples. Field samples are coded as with (1) or without (0) burning or nitrogen enrichment.
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Title Specimen-based data
Downloaded 8 times
Description This comma-delimited file contains the raw abundance (individuals per 100g) for each of 28 families for 64 field samples (16 plots x 2 seasons x 2 reps). Field samples are coded as with (1) or without (0) burning or nitrogen enrichment.
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Title Region 1 (subsamples "A") raw 454 sequencing reads
Downloaded 77 times
Description Text files with all raw 454 amplicon sequencing reads from region 1, containing all "A" subsamples, in FastA format. This is one of the datafiles (along with "region 2") used for pre-processing with the python script "amPy30.py"
Download TCA.454Reads.zip (61.53 Mb)
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Title Amplicon sequencing pipeline
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Description BASH script used to call sequence processing programs. Internal dependencies: amPy30.py, blastAnalysis30.py. External dependencies: Requires cutadapt 1.0, USEARCH 5.1, ssaha2.
Download AmpSeqpipeline30.sh (2.033 Kb)
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Title amPy30
Downloaded 6 times
Description Python script used to pre-process raw sequencing reads. Calls on three data files: 2 raw sequencing read files in FastA format ("X.TCA.454Reads.fna"), and "barcodeIDs.txt"
Download amPy30.py (2.732 Kb)
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Title barcodeIDs
Downloaded 5 times
Description TXT file mapping the multiplex identifier barcodes from each read to their respective sample and subsample ID. Treatment information (season, burning, and nitrogen) are also indicated in the file.
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Title eukSSU
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Description Eukaryotic SSU databased used in this study. Called for by AmpSeqPpipeline30.sh.
Download eukSSU.fasta (89.52 Mb)
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Title blastAnalysis30
Downloaded 10 times
Description Python script used to process results of matching non-redundant sequencing reads to their database match. Called for by "AmpSeqpipeline30.sh"
Download blastAnalysis30.py (5.575 Kb)
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When using this data, please cite the original publication:

Darby BJ, Todd TC, Herman MA (2013) High-throughput amplicon sequencing of rRNA genes requires a copy number correction to accurately reflect the effects of management practices on soil nematode community structure. Molecular Ecology 22(21): 5456–5471. http://dx.doi.org/10.1111/mec.12480

Additionally, please cite the Dryad data package:

Darby BJ, Todd TC, Herman MA (2013) Data from: High-throughput amplicon sequencing of rRNA genes requires a copy number correction to accurately reflect the effects of management practices on soil nematode community structure. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.t8g16
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