seqyclean

[…] the male and female genome builds29 (accessions srx180259, srx180261, and srx180262) to identify putative x, y and autosomal scaffolds using relative sequencing coverage between the sexes. we used seqyclean version 1.8.10 to quality filter, adapter trim, and screen for common acinetobacter contaminants (accessions cp000521, acpn01000000). filtered reads were then mapped to the reference male […]

[…] was extracted from approximately 1,000 nematodes using a qiagen dneasy kit. samples were sequenced using a miseq pe250 run with an expected coverage of ∼10× per sample. reads were then cleaned with seqyclean, mapped against the wbcel215.70 (http://jan2013.archive.ensembl.org/caenorhabditis_elegans/info/index) using bowtie 2 v2.1.0, and variants were called with the samtools package […]