6. Identification of Complete Scaffolds in Draft Assemblies

Recently, Jorgensen et al. 2014 and Kothari et al. 2018 described informatics protocols for finding circular/complete plasmids in draft genomic assemblies:

• Hundreds of Circular Novel Plasmids and DNA Elements Identified in a Rat Cecum Metamobilome - Jorgensen et al 2014

• Large Circular Plasmids from Groundwater Plasmidomes Span Multiple Incompatibility Groups and Are Enriched in Multimetal Resistance Genes - Kothari et al 2018

Inspired and borrowing from these methods, we developed the program findCircularScaffolds.py to identify:

• Whether the beginning and end of scaffolds align with each other.
• The number of paired-end reads bridging two ends of the scaffold.

Usage for findCircularScaffolds.py

usage: findCircularScaffolds.py [-h] -s SAMPLE_ID -a ASSEMBLY -1 FORWARD_READS
                                -2 REVERSE_READS -o OUTPUT_DIR [-t THREADS]

	Program which uses bowtie2 reflexive mapping of reads and blastn reflexive 
        alignment of scaffolds to assess whether any scaffolds in a sample's 
        assembly are circular.
	
optional arguments:
  -h, --help            show this help message and exit
  -s SAMPLE_ID, --sample_id SAMPLE_ID
                        name of sample. "-" cannot be in name.
  -a ASSEMBLY, --assembly ASSEMBLY
                        Assembly (FASTA format).
  -1 FORWARD_READS, --forward_reads FORWARD_READS
                        forward reads of paired-end set (FASTQ format).
  -2 REVERSE_READS, --reverse_reads REVERSE_READS
                        reverse reads of paired-end set (FASTQ format).
  -o OUTPUT_DIR, --output_dir OUTPUT_DIR
                        specify output directory
  -t THREADS, --threads THREADS
                        threads for bowtie2