Pipeline publication

[…] ith the function makeqtl, followed by refinement with refineqtl. The QTL object was fitted with fitqtl, and we searched for evidence of additional QTL with addqtl. In the case of evidence for an additional QTL, a new QTL model was built and the process repeated. All calculations and plots were generated within the R environment., High quality genomic DNA was isolated from leaves of a P-type B. vulgaris individual using a DNeasy Plant Kit (Qiagen). An Illumina paired-end (PE) library with a mean fragment length of 316 bp was prepared from genomic DNA and sequenced on an Illumina HiSeq2000 as paired end libraries with a 100 cycles. Reads were aligned to the draft G-type reference genome using BWA, and duplicates marked using Picard Tools (http://broadinstitute.github.io/picard). The Genome Analysis Tool Kit (GATK) was used to generate a list of putative INDELS and perform re-alignments around these regions, and call putative INDELS and SNPs. In addition to aligning P-type reads we also aligned reads from the G-type. We called genotypes when the genotype quality score was at least 30 (Phred scale), and filtered for positions that were heterozygous in either P or G-type genomes, or represented fixed differences between both types. Variant annotation was performed with SNPeff, making use of the genome annotation to predict SNP effect types., This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession LXTM00000000. The version described in this paper is version LXTM01000000. Sequence variation between G- and P-type plants, and annotations, are available as tracks in the Barbarea vulgaris Genome Database, http://plen.ku.dk/Barbarea. Data referenced in this study are available in NCBI with the accession codes SRR1582492 and SRR1583630., How to cite this article: Byrne, S. L. et al. The genome sequence of Barbarea vulgaris facilitates the study of ecological biochemistry. Sci. Rep. 7, 40728; doi: 10.1038/srep40728 (2017)., Publ […]

Pipeline specifications

Software tools BWA, Picard, GATK, SnpEff
Organisms Beta vulgaris, Plutella xylostella
Chemicals Glucosides, Thioglycosides, Saponins