Data from: Exploring origins, invasion history and genetic diversity of Imperata cylindrica (L.) P. Beauv. (Cogongrass) in the United States using genotyping by sequencing

Burrell AM, Pepper AE, Hodnett G, Goolsby JA, Overholt WA, Racelis AE, Diaz R, Klein PE

Date Published: March 19, 2015

DOI: http://dx.doi.org/10.5061/dryad.k2d05

 

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Title Cogongrass_449G__2320M_US_072514
Downloaded 39 times
Description SNP/INDEL data for 449 genotypes with 2320 markers
Download Cogongrass_449G__2320M_US_072514.xlsx (3.364 Mb)
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Title Imperata accession collection data
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Description This file contains the accession numbers of accessions sequenced and used in this manuscript. Data detailing the location in which the accessions were collected is also included.
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Title add_genotype-linenumber_file script
Downloaded 10 times
Description add_genotype-linenumber_file: This python script works on csv files that have been exported from the CLC Genomics Workbench. It adds two columns (genotype and line number) at the beginning of each csv file listed in column 1 of an input file. The input file is a csv file. The first row of the input file is considered as a header row. The script also removes the term "mapping" from the chromosome names.
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Title remove_header script
Downloaded 5 times
Description This python script removes the header row from each csv file that is listed in column 1 of an input csv file.
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Title merge_sort_enzymes_files
Downloaded 9 times
Description This perl script merges files listed in column 1 of an input csv file based on various columns within the files to be merged. For example, if chromosome number is found in column 3 and SNP position in column 4, the user could merge all files within the list by columns 3 and then by column 4.
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Title extract_SNPs_from_CLC_file
Downloaded 13 times
Description This python script cleans up the output files that come from the version 6.0 and higher of the CLC software. It removes any SNP calls with length greater than 1 and also all calls where the reference base is a deletion (i.e. a -). It also removes any duplicate entries in the input file.
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Title extract_SNPs_from_CLC_file script
Downloaded 8 times
Description This python script extracts unique and repetitive rows from an input csv file and puts them into two separate files.
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Title remove_offsite_SNPs script
Downloaded 4 times
Description This python script detects those SNPs that aren't within the specific distance of the restriction enzyme used for GBS DNA template preparation and puts good-hits and bad-hits into separate files.
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Title merge_CLCv6_SNP_files_with_SAM_files script
Downloaded 7 times
Description This python script merges the SNP detection results of CLC(version6 or higher) with the information in SAM files from CLC version 6 or higher. This script requires samtools. The user must specify the path to the samtools software path as well as the reference file name on lines 438 and 439 of this script.
Download merge_CLCv6_SNP_files_with_SAM_files.txt (16.66 Kb)
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When using this data, please cite the original publication:

Burrell AM, Pepper AE, Hodnett G, Goolsby JA, Overholt WA, Racelis AE, Diaz R, Klein PE (2015) Exploring origins, invasion history and genetic diversity of Imperata cylindrica (L.) P. Beauv. (Cogongrass) in the United States using genotyping by sequencing. Molecular Ecology 24(9): 2177-2193. http://dx.doi.org/10.1111/mec.13167

Additionally, please cite the Dryad data package:

Burrell AM, Pepper AE, Hodnett G, Goolsby JA, Overholt WA, Racelis AE, Diaz R, Klein PE (2015) Data from: Exploring origins, invasion history and genetic diversity of Imperata cylindrica (L.) P. Beauv. (Cogongrass) in the United States using genotyping by sequencing. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.k2d05
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