A toolbox for improving population genomes.
<b>[This project is in active development and not currently recommended for public use.]</b>
RefineM is a set of tools for improving population genomes. It provides methods designed to improve the completeness of a genome along with methods for identifying and removing contamination. RefineM comprises only part of a full genome QC pipeline and should be used in conjunction with existing QC tools such as [CheckM](https://github.com/Ecogenomics/CheckM/wiki). The functionality currently planned is:
<i>Improve completeness:</i> * identify contigs with similarity to specific reference genome(s) * identify contigs with compatible GC, coverage, and tetranucleotide signatures * indetify partial population genomes which should be merged together (requires [CheckM](https://github.com/Ecogenomics/CheckM/wiki))
<i>Reducing contamination:</i> * taxonomically classify contigs within a genome in order to identify outliers * identify contigs with divergent GC content, coverage, or tetranucleotide signatures * identify contigs with a coding density suggestive of a Eukaryotic origin
The simplest way to install this package is through pip: > sudo pip install refinem
This package requires numpy to be installed and makes use of the follow bioinformatic packages:
[prodigal](http://prodigal.ornl.gov/): Hyatt D, Locascio PF, Hauser LJ, Uberbacher EC. 2012. Gene and translation initiation site prediction in metagenomic sequences. <i>Bioinformatics</i> 28: 2223-2230.
[blast+](http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download): Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. 2009. BLAST+: architecture and applications. <i>BMC Bioinformatics</i> 10:421: doi: 10.1186/1471-2105-10-421.
[diamond](http://ab.inf.uni-tuebingen.de/software/diamond/) Buchfink B, Xie C, Huson DH. 2015. Fast and sensitive protein alignment using DIAMOND. <i>Nature Methods</i> 12: 59–60 doi:10.1038/nmeth.3176.
[krona](http://sourceforge.net/p/krona/home/krona/) Ondov BD, Bergman NH, and Phillippy AM. 2011. Interactive metagenomic visualization in a Web browser. <i>BMC Bioinformatics</i> 12: 385.
If you find this package useful, please cite this git repository (https://github.com/dparks1134/refinem)
Copyright © 2015 Donovan Parks. See LICENSE for further details.
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