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AWA - Copyright (C) 2017 - Denis Jacob Machado
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version 20170413
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# i. AVAILABILITY
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AWA comes with **ABSOLUTELY NO WARRANTY!** AWA is available at www.ib.usp.br/grant/anfibios/researchSoftware.html and https://gitlab.com/MachadoDJ/awa.
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The programs may be freely used, modified, and shared under the GNU General Public License version 3.0 (GPL-3.0, http://opensource.org/licenses/GPL-3.0).
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See LICENSE.txt for complete information about terms and conditions.
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Also, check the wiki page that are available at https://gitlab.com/MachadoDJ/awa/wikis/home/.
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# ii. CONTACT
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Author: Denis Jacob Machado
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Homepage: http://about.me/machadodj
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Email: denisjacobmachado@gmail.com
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Our lab's website: http://www.ib.usp.br/grant/anfibios
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# iii. SUMMARY
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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.
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# 1. DEPENDENCIES
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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 have problems.
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The program awa-trim can be used as a stand-alone application.
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The programs awa-map and awa-boot require a working installation of Bowtie2 (see http://bowtie-bio.sourceforge.net/bowtie2/index.shtml).
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# 2. BEFORE START USING AWA
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Keep in mind this is beta software that was designed very specifically to test the circularity of mitogenomes assemblies performed with MITObim (https://github.com/chrishah/MITObim).
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Reads must be provided as .fastq file. Entries must be interleave.
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Reference sequence must be provided as a single .fasta file.
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# 3. WHAT IS INSIDE
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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.
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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.
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The program awa-boot 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.
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A complete tutorial with example files in currently being prepared and should be available soon.
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# 4. CITE
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Machado D.J., Janies D., Grant T. (in prep.) . **Four New Complete Mitochondrial Genomes of Frogs with Comments on Circularity Inference**. *Mitochondrial DNA Part A*. |