Computational protocol: iSeq: A New Double-Barcode Method for Detecting Dynamic Genetic Interactions in Yeast

Similar protocols

Protocol publication

[…] Strains were streaked for single colonies from frozen stocks, and grown up overnight in YPD at 30°. Genomic DNA was isolated with the YeaStar Genomic DNA Kit (Zymo Research). Libraries for Illumina sequencing were constructed in 96-well format as previously described (), pooled and analyzed for quality using Bioanalyzer (Agilent Technologies) and Qubit (Life Technologies), and sequenced on one lane of Illumina HiSeq 2000. Reads were trimmed for adaptors, quality and minimum length with cutadapt 1.7.1 (). Reads were mapped to the reference genome with BWA version 0.7.10-r789 (). And variants were called with GATK’s Unified Genotyper v.3.3.0 (). Significant changes in copy number were discovered using the CNV-Seq package (). SIFT was used to predict the protein function tolerance of amino acid changes resulting from SNPs verified by visual inspection using samtools tview and mpileup (; ). […]

Pipeline specifications

Software tools cutadapt, BWA, GATK, CNV-seq, SIFT, SAMtools tview, SAMtools
Application WGS analysis
Organisms Saccharomyces cerevisiae