Trimmed reads used for the de novo assembly of the Klebsiella phage RSU-F4K5 genome
Total DNA was extracted from a lysate filtrate of phage RSU-F4K5 using Proteinase K/SDS treatment and Genomic DNA Clean & Concentrator-10 Kit (Zymo Research). Approximately 200 ng of the extracted dsDNA were subjected to ultrasonication in a microTUBE AFA Fiber Pre-slit Snap-Cap 6x16mm (Covaris) using S220 focused-ultrasonicator (Covaris) as a means of random fragmentation with the settings for a target average fragment length of 550 bp. Fragmented DNA was then used as input to prepare Illumina MiSeq-compatible DNA libraries for 250 bp paired-end read sequencing using the TruSeq DNA Nano Low Throughput Library Prep Kit (Illumina) as per the manufacturer's instructions (using adapter #22 from the TruSeq DNA Single Indices Set B (Illumina)). The resultant library was sequenced on the Illumina MiSeq system as one of the several individually barcoded pooled libraries using 500-cycle MiSeq Reagent Kit Nano v2 (including PhiX sequencing control). Demultiplexed reads first had the possible adapter remnants trimmed. Next, reads matching the sequence of phiX 174 genome (sequencing control) were discarded.  Lastly, reads were length and quality-trimmed. All the trimming of the dataset was performed using bbduk from the BBmap package.
SUB15142522
RSU-F4K5