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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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AWA comes with ABSOLUTELY NO WARRANTY!
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AWA is available at
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www.ib.usp.br/grant/anfibios/researchSoftware.html and
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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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The programs may be freely used, modified, and shared
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under the GNU General Public License version 3.0
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(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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See LICENSE.txt for complete information about terms and
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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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Also, check the wiki page that are available at
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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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* 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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The “AWA” project integrates software solutions for testing
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the completeness of assemblies of circular DNA based on
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short sequence reads. A new version of AWA is currently
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being prepared and will accompany a discussion of its
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applications for all types of circular DNA. The current
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version should be considered a draft and has only been
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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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AWA was written in Python v3.5.1 on a macOS v10.12.4 and has
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not being tested in other platforms. The program should run
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on any UNIX based system, but contact the author if you
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have problems.
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The program awa-trim can be used as a stand-alone application.
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The program awa-trim can be used as a stand-alone
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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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The programs awa-map and awa-boot require a working
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installation of Bowtie2 (see
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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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Keep in mind this is beta software that was designed very
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specifically to test the circularity of mitogenomes
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assemblies performed with MITObim
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(https://github.com/chrishah/MITObim).
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Reads must be provided as .fastq file. Entries must be interleave.
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Reads must be provided as .fastq file. Entries must be
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interleave.
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Reference sequence must be provided as a single .fasta file.
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Reference sequence must be provided as a single .fasta
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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. INSTALLATION
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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.
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# 5. CITE
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Please cite the program page while publication is getting redy. |
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The program awa-trim searches for the largest possible
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circular DNA fragment inside the presented scaffold by means
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of searching from matching words with a minimum length that
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are at a minimum distance from each other.
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The program awa-map leverages on Bowtie2. It maps the reads
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back to the potential circular DNA fragment, flipping the
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fragment so its original end will be together at the middle
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of the fragment. The program reports many statistics focused
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on the 100 pb in the middle of the flipped sequence
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fragment. All this stats are know, except for the contiguity
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coverage, which measures the amount of reads that supports
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the position of a nucleotides in relation to its two
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adjacent neighbors. The program will not say if the DNA is
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circular, it will only provide information necessary for the
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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
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sensitive the program is to random deletion or addition of
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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
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prepared and should be available soon.
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# 4. INSTALL
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As it is, download awa scripts and the awa_module folder to
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your computer, make the scripts executable, and add them to
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your PATH. Make sure the awa_module folder is in the same
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directory as the 3 awa scripts.
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# CITE
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Machado D.J., Janies D., Brouwer C. R., & Grant T.(under
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review). Four New Complete Mitochondrial Genomes of Frogs
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and a New Strategy to Infer Circularity. _Ecology and
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Evolution_ (submitted Sep. 9, 2017). |