The “AWA” project integrates software solutions for testing
the completeness of assemblies of circular DNA based on
short sequence reads. A new version of AWA is currently
being prepared and will accompany a discussion of its
applications for all types of circular DNA. The current
version should be considered a draft and has only been
tested for mitogenome assemblies of frog DNA.
AWA was written in Python v3.5.1 on a macOS v10.12.4 and has
not being tested in other platforms. The program should run
on any UNIX based system, but contact the author if you
The program awa-trim can be used as a stand-alone
Keep in mind this is beta software that was designed very
specifically to test the circularity of mitogenomes
assemblies performed with MITObim
Reads must be provided as .fastq file. Entries must be
Reference sequence must be provided as a single .fasta
3. WHAT IS INSIDE
The program awa-trim searches for the largest possible
circular DNA fragment inside the presented scaffold by means
of searching from matching words with a minimum length that
are at a minimum distance from each other.
The program awa-map leverages on Bowtie2. It maps the reads
back to the potential circular DNA fragment, flipping the
fragment so its original end will be together at the middle
of the fragment. The program reports many statistics focused
on the 100 pb in the middle of the flipped sequence
fragment. All this stats are know, except for the contiguity
coverage, which measures the amount of reads that supports
the position of a nucleotides in relation to its two
adjacent neighbors. The program will not say if the DNA is
circular, it will only provide information necessary for the
user to make that decision based on his own criteria.
The program awa-bootstrap is used by developers to see how
sensitive the program is to random deletion or addition of
bases on the 100 pb in the middle of the flipped sequence.
A simple tutorial with example files in currently being
prepared and should be available soon.
As it is, download awa scripts and the awa_module folder to
your computer, make the scripts executable, and add them to
your PATH. Make sure the awa_module folder is in the same
directory as the 3 awa scripts.
Machado D.J., Janies D., Brouwer C. R., & Grant T.(under
review). Four New Complete Mitochondrial Genomes of Frogs
and a New Strategy to Infer Circularity. Ecology and
Evolution (submitted Sep. 9, 2017).