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Pipeline publication

[…] be this variation to make predictions for how TEs affect the functions of genes, so wild strains with TE insertions into specific genes provide mutant alleles for future studies. Given the power of C. elegans to map the genes that control quantitative traits (; ; ; ; ; ; ), these data will provide both the markers to help identify quantitative trait genes and the functional variants that could underlie complex traits., Whole-genome sequence data was obtained from 208 C. elegans strains as described previously (). In brief, paired-end 100 bp sequencing was conducted using the Illumina HiSeq 2500 system, and sequences were demultiplexed and trimmed using the fastx barcode splitter tool of the FASTX-Toolkit v0.0.14 (http://hannonlab.cshl.edu/fastx_toolkit/) and Trimmomatic v0.32 (). Trimmed reads were aligned to the WS245 reference genome (http://www.wormbase.org) with BWA v0.7.8-r455 (). Strains with concordance greater than 99.93% were grouped together as the same genome-wide haplotype, as done previously (; ). This grouping left 152 unique strains in our analysis set (see supplemental file S1 in ). All raw reads are deposited in the Sequence Read Archive with project number PRJNA318647. Alignment and variant call format (VCF) files are available from the C. elegans Natural Diversity Resource (CeNDR, http://www.elegansvariation.org/Data) ()., The ability to identify transposons and quantify transposon copy number often relies on a well curated set of transposon consensus sequences and annotated positions of transposons in the reference genome. Consensus […]

Pipeline specifications

Software tools FASTX-Toolkit, Trimmomatic, BWA
Databases WormBase