metaMix protocols

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metaMix specifications

Information


Unique identifier OMICS_09072
Name metaMix
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 0.2
Stability Stable
Requirements
Matrix, ggplot2, gtools, knitr, R(≥3.0.1), data.table(≥1.9.2), Rmpi
Maintained Yes

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Documentation


Maintainer


  • person_outline Sofia Morfopoulou <>

Publication for metaMix

metaMix in pipelines

 (2)
2016
PMCID: 5209397
PMID: 27770235
DOI: 10.1007/s00401-016-1629-y

[…] as well as all the bacteria of the human microbiome, according to ftp://ftp.ncbi.nih.gov/genomes/human_microbiom/bacteria/all.faa.tar.gz. the blastx results were the input of metamix []., for the analysis of the vaccine sequencing, we first removed 15 % of the reads as duplicates and merged overlapping reads. we trimmed the reads based on base quality (q = 20) using trim […]

2016
PMCID: 5209397
PMID: 27770235
DOI: 10.1007/s00401-016-1629-y

[…] reference database., we performed de novo assembly with spades [] followed by quast [] for both the vaccine and the brain sequencing data. in the latter case, we used the muv reads as identified by metamix []. novoalign, samtools [] and varscan2 [] were used for consensus sequence generation and variant calling. we filtered variants based on quality, depth, frequency and strand bias (quality […]


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metaMix in publication

PMCID: 5209397
PMID: 27770235
DOI: 10.1007/s00401-016-1629-y

[…] as well as all the bacteria of the human microbiome, according to ftp://ftp.ncbi.nih.gov/genomes/human_microbiom/bacteria/all.faa.tar.gz. the blastx results were the input of metamix []., for the analysis of the vaccine sequencing, we first removed 15 % of the reads as duplicates and merged overlapping reads. we trimmed the reads based on base quality (q = 20) using trim […]


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metaMix institution(s)
UCL Genetics Institute, University College London, London, UK

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