Commit 7ca828c2 authored by Denis Jacob Machado's avatar Denis Jacob Machado

Update README.txt

parent 8d6a751c
......@@ -2,9 +2,9 @@ AWA - Copyright (C) 2017 - Denis Jacob Machado
version 20170413
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i. AVAILABILITY
# i. AVAILABILITY
AWA comes with ABSOLUTELY NO WARRANTY!
AWA is available at
......@@ -21,18 +21,18 @@ conditions.
Also, check the wiki page that are available at
https://gitlab.com/MachadoDJ/awa/wikis/home/.
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ii. CONTACT
# ii. CONTACT
Author: Denis Jacob Machado
Homepage: http://about.me/machadodj
Email: denisjacobmachado@gmail.com
Our lab's website: http://www.ib.usp.br/grant/anfibios
* Author: Denis Jacob Machado
* Homepage: http://about.me/machadodj
* Email: denisjacobmachado@gmail.com
* Our lab's website: http://www.ib.usp.br/grant/anfibios
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iii. SUMMARY
# iii. SUMMARY
The “AWA” project integrates software solutions for testing
the completeness of assemblies of circular DNA based on
......@@ -42,9 +42,9 @@ 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
# 1. DEPENDENCIES
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
......@@ -58,9 +58,9 @@ 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
# 2. BEFORE START USING AWA
Keep in mind this is beta software that was designed very
specifically to test the circularity of mitogenomes
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Reference sequence must be provided as a single .fasta
file.
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3. WHAT IS INSIDE
# 3. WHAT IS INSIDE
The program awa-trim searches for the largest possible
circular DNA fragment inside the presented scaffold by means
......@@ -101,19 +101,20 @@ bases on the 100 pb in the middle of the flipped sequence.
A complete tutorial with example files in currently being
prepared and should be available soon.
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4. INSTALL
# 4. INSTALL
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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CITE
# CITE
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.
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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).
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