Ipyrad pipeline parameters files, raw sequence data, barcodes and supporting scripts for clonal and cytotype sample assignment of Populus tremuloides.



Document Type




File Format

.fastq, .py, .txt, .R

Viewing Instructions

This data set contains the following: 1. Raw compressed amplicon sequence data (fastq.gz) from 3 individual Illumina HiSeq2500 lanes ("BP01", "BP02" and "BP03"). Each lane is presented here in 7 individual sequencing files "aa" to "ag" for ease of data transfer. Once download the command line instructions in the README can be used to compile the required fastq.gz files for downstream analysis (p1815-BP01_S40_L006_R1_001.fastq.gz, p1815-BP02_S41_L007_R1_001.fastq.gz and p1815-BP03_S42_L008_R1_001.fastq.gz). 2.Barcode files corresponding to each raw amplicon sequence data file (barcodes01.txt, barcodes02.txt and barcodes03.txt). 3. Ipyrad (http://ipyrad. readthedocs. io) parameters files used to run steps 2 thru 7 of Ipyrad. Separate sequence files were demultiplexed in step 1 of Ipyrad then merged prior to running remaining steps. One parameters file to be subsequently used for clonal assignment (params-BP123_XXXXXXXX_clone.txt) and the other for cytotype analysis (params-BP123_XXXXXXXX_ploidy.txt). 4. Python script to remove a list of individuals from .vcf files for downstream analysis ( 5. R script to transform jaccard pair-wise similarity indices to clonal group assignments (clone_assignment.R). Additionally, the following scripts were implemented as part of this pipeline: 1. vcf2Jaccard (, Carol Rowe) 2. vcf2hetAlleleDepth (, Carol Rowe) 3. gbs2ploidy (Gompert, Z., Mock, K. Detection of individual ploidy levels with genotyping-by-sequencing (GBS) analysis. Mol. Eco. Res. 17:1156-67.)

Publication Date



Arizona State University School of Life Sciences


Utah State University


Leaf samples (n=503) were collected from three watersheds in southwestern Colorado. Genomic DNA was subsequently extracted and a ddRAD library prepared following Parchmen et al. 2012. Individually barcoded samples were then pooled and sequenced in three separate libraries using an Illumina HiSeq2500. Additional details can be found in the forthcoming publication.

Scientfic Names

Populus tremuloides




Exact instructions for concatenating the files are included in the README file.


Botany | Genetics


Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 License.



Additional Files

README.txt (4 kB)
MD5: 60852e01432ed70e06a2e0fb22226754

barcodes01.txt (4 kB)
MD5: 740ebcfd2c95f14a1a7f9e89156884f5

barcodes02.txt (4 kB)
MD5: 88deeceb758249a37df01677d7d0eda6

barcodes03.txt (3 kB)
MD5: 0d8a192bdff6865c4f34b9f356633a26

msl_10_Parameters.txt (3 kB)
MD5: f8e392a2d34133ba5c2fb430164b09ab

msl_250_Parameters.txt (3 kB)
MD5: f8e392a2d34133ba5c2fb430164b09ab

BP01_S40_L006_R1_aa.fastq.gz (1860416 kB)
MD5: fd1d44ad9bee923f0e4d38b32a02ac04

BP01_S40_L006_R1_ab.fastq.gz (1836351 kB)
MD5: a4f5b31ecbb3fc56e596b74edda52151

BP01_S40_L006_R1_ac.fastq.gz (1859417 kB)
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BP01_S40_L006_R1_ad.fastq.gz (1956087 kB)
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BP01_S40_L006_R1_ae.fastq.gz (2009013 kB)
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BP01_S40_L006_R1_af.fastq.gz (1986107 kB)
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BP01_S40_L006_R1_ag.fastq.gz (1226263 kB)
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BP02_S41_L007_R1_aa.fastq.gz (1850345 kB)
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BP02_S41_L007_R1_ab.fastq.gz (1826515 kB)
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BP02_S41_L007_R1_ac.fastq.gz (1873673 kB)
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BP02_S41_L007_R1_ad.fastq.gz (1990780 kB)
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BP02_S41_L007_R1_ae.fastq.gz (1968924 kB)
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BP02_S41_L007_R1_af.fastq.gz (2032458 kB)
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BP02_S41_L007_R1_ag.fastq.gz (669386 kB)
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BP03_S42_L008_R1_aa.fastq.gz (1840608 kB)
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BP03_S42_L008_R1_ab.fastq.gz (1845704 kB)
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BP03_S42_L008_R1_ac.fastq.gz (1901644 kB)
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BP03_S42_L008_R1_ad.fastq.gz (2020478 kB)
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BP03_S42_L008_R1_ae.fastq.gz (2000875 kB)
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BP03_S42_L008_R1_af.fastq.gz (2117778 kB)
MD5: 0b519e03916f8f55efb502fc7a1ec8be

clone_assignment.R (1 kB)
MD5: c1e503ce99749650f3fb1e18083f177f

BP03_S42_L008_R1_ag.fastq.gz (209154 kB)
MD5: a31f17c8fcd2ee0fa4cae22e6c0380e9 (1 kB)
MD5: b058790fd20812b7265d5b9a731cde82

msl_10_lessDroppedInds.vcf (1454636 kB)
MD5: 4e622dfc6f77ab3d182670b65821bbe3

msl_250_lessDroppedInds.vcf (108375 kB)
MD5: cd6095ef2d640585304f4b9717f3622b

Results.xlsx (123 kB)
MD5: ff3bd7f8203137ff0c5b2ac171e73700

estploidy_pp98.csv (35 kB)
MD5: 37ab3edd0f585c444070de6c426f30c8

2019-02-13-01 Walton_pre.pdf (264 kB)
MD5: 8b06813217ca3c3dc044a852c719c8bb

2019-02-14-01 Walton_post.pdf (244 kB)
MD5: 5bf02e0c4f2bc05036d61a06fd82ded9