adapter_barcode_ID
AD006
barcode_seq
GCCAAT
processing_pipeline
Whole genome shotgun sequencing was performed on the Illumina HiSeq2500 platform (100 x 100 bp paired end read lengths, rapid run mode) using TruSeq v3 cluster kits and TruSeq sequencing-by-synthesis (SBS) chemistry (Illumina) at the Penn Genomic Frontiers Institute (PGFI) at the University of Pennsylvania. DNA FASTQ read files were processed using FastQC v0.11.27 to review read lengths, quality scores, k-mer over-representation, adapter enrichment, and number of duplicate reads. Reads were trimmed using Trimmomatic v0.328 to remove adapter read-through, palindromic artifacts, low quality bases, and successive ambiguous base calls while also maintaining paired-end read ordering. The Illumina adapter-specific clipping strategy was performed using specific adapter lists for TruSeq libraries (please refer to supplemental files in associated publication). Clipping required an average quality of 20 over a sliding window of four nucleotides. Leading and trailing bases were required to have quality scores of three or higher, and only DNA reads with lengths of at least 25 bases were retained.
seq_center
PGFI
machine_ID
ST431
run_ID
58489
seq_chemistry
TruSeq v3 clustering, TruSeq SBS
fastq_encoding
illumina_1.9_sanger
software
CASAVA-1.8.2, RTA-1.17.21.3, HiSeqControlSoftware-2.0.10.0