The genomic DNA library of Csp_BJ was constructed by using a QIAseq FX DNA Library Kit (Qiagen) according to the manufacturer’s instructions, and then by paired-end sequencing using an Illumina NextSeq 500 platform with a 300-cycle NextSeq 500 reagent kit v2 (Illumina). The metagenomic samples were sequenced by single-end sequencing by using a 150-cycle NextSeq 500 reagent kit v2 (Illumina). The complete genome sequence of the strain was determined by using a PacBio Sequel (Pacific BioSciences) sequencer with a Sequel SMRT Cell 1M v2 (four/tray) and a Sequel sequencing kit v2.1 (Pacific BioSciences) for long-read sequencing (insert size, ≈10 kb). High quality genomic DNA was used to prepare a SMRTbell library by using a SMRTbell Template Prep Kit 2.0 (Pacific Biosciences). The draft genome contigs were assembled by using A5-Miseq software with Illumina short reads [33 (link)]. The circular genome sequence was constructed by using Canu version 1.4 [34 (link)], Minimap version 0.2-r124 [35 (link)], racon version 1.1.0 [36 (link)], and Circlator version 1.5.3 [37 (link)] with long read data. Error correction of the circular sequence was performed by using Pilon version 1.18 with short reads [38 (link)]. Annotation was performed in DFAST version 1.0.8 [39 (link)] and NCBI-BLASTP/BLASTX against deposited Chromobacterium complete genome sequences.
Sequel sequencing kit v2
Manufactured by Pacific Biosciences
The Sequel sequencing kit v2.1 is a reagent kit designed for use with the Sequel System, a DNA sequencing platform developed by Pacific Biosciences. The kit provides the necessary reagents and consumables required to perform long-read, single-molecule, real-time (SMRT) DNA sequencing on the Sequel System.
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Lab products found in correlation
Nextseq 500 reagent kit v2, by Illumina (1 mentions)
Smrtbell template prep kit 2, by Pacific Biosciences (1 mentions)
Short read, by Illumina (1 mentions)
Qiaseq fx dna library kit, by Qiagen (1 mentions)
Nextseq 500 platform, by Illumina (1 mentions)
Pacbio sequel, by Pacific Biosciences (1 mentions)
Smrtbell express template prep kit, by Pacific Biosciences (1 mentions)
Bluepippin, by Sage Science (1 mentions)
2 protocols using sequel sequencing kit v2
1
Csp_BJ Genome Sequencing and Annotation
2
Long-Read Sequencing of Esperanza's Lung DNA
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Genomic DNA was extracted from Esperanza's lung tissue using the high salt extraction method as described previously [26 (link)]. The DNA was converted into sequencing libraries using the SMRTbell Express Template Prep Kit (Pacific Biosciences, Menlo Park, CA) as directed, except without any shearing step. Three libraries were prepared, 1 with a 25-kb cut-off setting on the BluePippin instrument (Sage Science, Beverly, MA) and 2 with a 30-kb cut-off setting. The libraries were sequenced with 44 cells on a Sequel instrument (Pacific Biosciences Sequel System, RRID:SCR_017989 ) using Sequel Sequencing kit v2.1 chemistry (Pacific Biosciences, Menlo Park, CA).
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