This is the Linux app named mitoMaker to run in Linux online whose latest release can be downloaded as mitoMaker_1.14.tar.gz. It can be run online in the free hosting provider OnWorks for workstations.
Download and run online this app named mitoMaker to run in Linux online with OnWorks for free.
Follow these instructions in order to run this app:
- 1. Downloaded this application in your PC.
- 2. Enter in our file manager https://www.onworks.net/myfiles.php?username=XXXXX with the username that you want.
- 3. Upload this application in such filemanager.
- 4. Start the OnWorks Linux online or Windows online emulator or MACOS online emulator from this website.
- 5. From the OnWorks Linux OS you have just started, goto our file manager https://www.onworks.net/myfiles.php?username=XXXXX with the username that you want.
- 6. Download the application, install it and run it.
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mitoMaker to run in Linux online
DESCRIPTION
mitoMaker is a pipeline script developed to simplify the assembly and automatic annotation of mitochondrial genomes, based on raw NGS reads and an optional target reference.mitoMaker calls well known assemblers and algorithms, such as SOAPdenovo, MIRA and blast+ and parses their results providing easily readable outputs, such as FASTA, GENBANK, SEQUIN, PNG and others.
General pipeline:
1-iterative De Novo assembly, with different k-mer values, trying to assemble a build that matches a target mitochondrial genome given.
2-searches for all mitochondrial gene features and circularization.
3-stores the best result found.
4-uses the best assembly as backbone for a reference based assembly, using MIRA and MITObim, trying to extend the mitogenome and close gaps.
5-annotates the best assembly, identifying the start and end position of each and every feature.
6-creates a folder with all the results (PNG, GENBANK, FASTA, SEQUIN, CAF, MAF and a stats logfile).
Features
- Automatic annotation of mitochondrial genomes
- Automatic assembly b ased on raw reads
- Very customizable through command line
Audience
Science/Research
User interface
Console/Terminal
Programming Language
Python
This is an application that can also be fetched from https://sourceforge.net/projects/mitomaker/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.
