CCBGpipe

CCBGpipe completes circular bacterial genomes from Oxford Nanopore MinION long-read sequencing data by automating de novo assembly, polishing, circularization, deduplication, and rearrangement to produce accurate linear representations of circular genomes.

Key Features:

• Automated workflow: Automates processing from raw MinION data through assembly and polishing to produce assembled contigs.
• Sampling strategy for de novo assembly: Performs multiple assemblies using a sampling strategy to generate circular contigs with overlapping sequences at contig termini.
• Polishing using raw signal and reads: Polishes circular contigs using raw signal data and sequencing reads to improve sequence accuracy.
• Deduplication and linearization: Removes duplicated terminal overlaps and produces a linear representation of the circular genome.
• Circularization and rearrangement: Rearranges circularized contigs to start at dnaA/repA or other replication origins determined by GC skew analysis.
• Implementation: Implemented in Python.

Scientific Applications:

• Completion of multiple bacterial genomes from a single run: Demonstrated by completing circular genomes of 12 bacterial species from one MinION sequencing run.
• Chromosome and plasmid reconstruction: Produced 48 complete circular sequences comprising 12 chromosomes and 36 plasmids, including Acinetobacter nosocomialis, Acinetobacter pittii, and Staphylococcus aureus.
• High-coverage assemblies: Produces complete assemblies with adequate read coverage (~80×), supporting genomic studies of organisms with circular genomes.

Methodology:

Demultiplexing and base calling of raw MinION current signals; multiple de novo assemblies using a sampling strategy to produce circular contigs with terminal overlaps; polishing using raw signal data and sequencing reads; removal of duplicated sequences and linearization; circularization and rearrangement to start positions based on GC skew analysis and dnaA/repA detection.