Plastidmaker

beta

mitoMaker - a mitochondria pipeline wrapper script

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Description

Mitomaker is a pipeline wrapper, result analyzer and automated annotator, written in Python v2.7, that, with the help of other programs, builds, analyzes, looks for the best build and annotates target genomes (such as mitochondria and cloroplast). It could be used with other targets, such as specific genes, or transcriptomes, even though that is not it's primary goal, nor thoroughly tested.

After various attempts to build different mitochondrial genomes in the lab I studied, a general pipeline started to appear: assemble reads with MIRA or SOAPdenovo-Trans, look for a scaffold/contig that matches a closely-related species, check it to see if all expected genomic features are present (since mitochondria is well conserved), check to see if the assembly might have circularized (since it's a circular DNA). If a feature was missing, or it hasn't circularized, try and assemble again with different assembler parameters (mainly k-mer). Rinse and repeat until the best build is found.

Plastidmaker Web Site

Categories

Bio-Informatics

License

MIT License

Features

  • Bioinformatics
  • Plastid building automated pipeline
  • Genomic analyzer
  • Plastid assembly

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Additional Project Details

Languages

English

Intended Audience

Science/Research

User Interface

Console/Terminal

Programming Language

Python

Registered

2014-05-19
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