plasmid sequencing service  (Plasmidsaurus)

Journal: PLOS One

Article Title: Sequencing complete plasmids on Oxford Nanopore Technologies sequencers using R2C2 and Chopper

doi: 10.1371/journal.pone.0345168

Figure Lengend Snippet: Plasmids were processed with rolling circle amplification (RCA) to produce linear DNA containing multiple tandem repeats of the original plasmids. The linear DNA was prepped and sequenced on an ONT P2Solo. The resulting ONT data were then processed into ONT reads by dorado and consensus reads by an updated version of C3POa. Consensus reads and subreads originating from multiple reads covering the same plasmid were then combined into one highly accurate plasmid sequence using the newly developed Chopper.

Article Snippet: To determine if commercial plasmid sequencing services would struggle with these homopolymers as well, we sent all four plasmids in this study to Plasmidsaurus for sequencing and analysis.

Techniques: Amplification, Plasmid Preparation, Sequencing

Journal: PLOS One

Article Title: Sequencing complete plasmids on Oxford Nanopore Technologies sequencers using R2C2 and Chopper

doi: 10.1371/journal.pone.0345168

Figure Lengend Snippet: For each sequencing run, the read length distributions of the raw ONT sequencing data (grey) and R2C2 consensus reads (blue) are shown as histograms. The length of sequenced plasmids (orange) included in each run is also shown.

Article Snippet: To determine if commercial plasmid sequencing services would struggle with these homopolymers as well, we sent all four plasmids in this study to Plasmidsaurus for sequencing and analysis.

Techniques: Sequencing

Journal: PLOS One

Article Title: Sequencing complete plasmids on Oxford Nanopore Technologies sequencers using R2C2 and Chopper

doi: 10.1371/journal.pone.0345168

Figure Lengend Snippet: Chopper accepts R2C2 consensus reads and their subreads produced by C3POa as input. It then bins R2C2 consensus reads by length to identify different plasmids in the sequencing data. For each length bin/plasmid, Chopper then generates a highly accurate plasmid sequence using racon and medaka for polishing.

Article Snippet: To determine if commercial plasmid sequencing services would struggle with these homopolymers as well, we sent all four plasmids in this study to Plasmidsaurus for sequencing and analysis.

Techniques: Produced, Sequencing, Plasmid Preparation

Journal: PLOS One

Article Title: Sequencing complete plasmids on Oxford Nanopore Technologies sequencers using R2C2 and Chopper

doi: 10.1371/journal.pone.0345168

Figure Lengend Snippet: Chopper was run on data from the 4 sequencing runs on individual plasmids. 100 R2C2 consensus reads were polished for each plasmid sequencing run (using the --iterations argument). Each R2C2 consensus read was polished with increasing numbers of R2C2 subreads (using the --subreads argument). With the exception of pSpCas9, Chopper produced almost entirely error-free sequences once more than 20 R2C2 subreads were used for polishing.

Article Snippet: To determine if commercial plasmid sequencing services would struggle with these homopolymers as well, we sent all four plasmids in this study to Plasmidsaurus for sequencing and analysis.

Techniques: Sequencing, Plasmid Preparation, Produced

Journal: PLOS One

Article Title: Sequencing complete plasmids on Oxford Nanopore Technologies sequencers using R2C2 and Chopper

doi: 10.1371/journal.pone.0345168

Figure Lengend Snippet: R2C2 subreads, R2C2 consensus reads, and Chopper sequences are aligned to the indicated plasmid references. Mismatches and Indels and are indicated in red, alignment ends in black B) . The error-rate of R2C2 consensus reads and Chopper sequences at specific positions of the pSpCas9 plasmid. These error-rates are shown as stacked bargraphs for a region of the plasmid that contains two homopolymers which represent a source for systematic sequencing error. C) Pairwise alignment of the pSpCas9 plasmid reference and the sequence Plasmidsaurus produced for that plasmid.

Article Snippet: To determine if commercial plasmid sequencing services would struggle with these homopolymers as well, we sent all four plasmids in this study to Plasmidsaurus for sequencing and analysis.

Techniques: Plasmid Preparation, Sequencing, Produced