adapter_barcode_ID
AD012
barcode_seq
CTTGTA
processing_pipeline
Whole genome shotgun sequencing was performed on the Illumina MiSeq platform (150 x 150 bp paired end read lengths) using TruSeq v3 cluster kits and TruSeq sequencing-by-synthesis (SBS) chemistry (Illumina) at the Next Generation Sequencing Core / Functional Genomics Core (NGSC/FGC) of the Perelman School of Medicine 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 MPv2 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. All long insert MPv2 jumping mate pair DNA library reads were processed using the program FastUniq v1.19 to remove the high proportion of low diversity or duplicate read pairs typical of mate pair libraries with increasingly longer insert sizes.
seq_center
FGC_NGSC
machine_ID
M00590
run_ID
FGC0460
seq_chemistry
TruSeq v3 clustering, TruSeq SBS
fastq_encoding
illumina_1.9_sanger
software
CASAVA-1.8.2, RTA-1.17.28, MiSeqControlSoftware-2.2.0