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Fig. 1 | BMC Bioinformatics

Fig. 1

From: Clustering of circular consensus sequences: accurate error correction and assembly of single molecule real-time reads from multiplexed amplicon libraries

Fig. 1

Graphical representation of the C3S-LAA process and pipeline. a Raw reads comprised of multiple subreads are depicted for three different amplicons [green, fuchsia and blue boxes; different shades of color are used to portray variable subread sequence qualities (darker shading portrays higher quality)]. Subreads are separated by a shared adapter sequence (grey boxes). The higher quality CCS read for each raw read is used to cluster the corresponding raw reads into CCS-based cluster groups. Error correction is performed per CCS-based cluster, producing top quality consequences sequences, followed by assembly of any overlapping consensus sequences. b A single run parameters file is used by all components of the pipeline. The grey highlighted rectangles represent two main steps of C3S-LAA. (i) Using the CCS reads generated by the SMRT analysis reads of insert protocol, C3S clusters the raw reads according to each barcode-primer pair combination, producing files of read identifiers to whitelist the corresponding raw reads. (ii) Raw read clusters are passed to Quiver to generate amplicon-specific consensus sequences, which are then passed to Minimus for sequence assembly. Rectangles with folded corners represent single files or multiple files (depicted as stacks of files) and those with rounded edges represent scripts and tools. Arrows indicates output files that are generated. Connecting lines with dots at one end depict input files, with the dot corresponding to the source data for the connected script or tool

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