Minia protocols

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Minia specifications


Unique identifier OMICS_00022
Name Minia
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux, Mac OS
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained Yes



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  • person_outline Rayan Chikhi <>

Publication for Minia

Minia in pipeline

PMCID: 5717231
PMID: 29214047
DOI: 10.1038/s41522-017-0043-0

[…] designated as novel c. difficile isolates were downloaded from the ncbi sequence read archive (see table  for accessions), trimmed for quality using trimmomatic and assembled into contigs using minia. contigs containing portions of 16s rrna genes were identified using blastn and extracted for amplicon simulations. for each isolate, we subsequently simulated 16s rrna amplicon sequence reads […]

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Minia in publications

PMCID: 5568732
PMID: 28829832
DOI: 10.1371/journal.pone.0183535

[…] there were other peaks with the regular model. therefore, different values of k (21, 47, 53, 71, 91) were used with their corresponding minimum abundance estimates to generate multiple assemblies. minia v1.6088; [] was used with sspace-standard v3.0 [] to assemble trimmed reads into gapped contigs. within sspace, bowtie v0.12.5 [] was used to map reads during “scaffolding” and without […]

PMCID: 5643016
PMID: 29114402
DOI: 10.1099/mgen.0.000123

[…] as reference and outgroup genomes (see table s1). the phylogeny of the considered strains is depicted in fig. s1 and is taken from []., we de novo assembled adna reads into contigs using minia [] for both adna data sets (london outbreak and marseille outbreak). minia is a conservative assembler based on an efficient implementation of the de bruijn graph methodology. in general, minia […]

PMCID: 4641413
PMID: 26555130
DOI: 10.1186/s13071-015-1198-2

[…] a local maximum, followed by one additional peak at k = 71, and a shoulder that dropped substantially after k = 101. thus, different values of k were used to generate multiple assemblies. minia (v1.6088; []) was used with sspace-standard (v3.0; []) to assemble trimmed reads into gapped contigs. within sspace, bowtie (v0.12.5; []) was used to map reads during “scaffolding” and without […]

PMCID: 4619942
PMID: 26539459
DOI: 10.1155/2015/196591

[…] error rate, memory requirement for representing k-mers might be prohibitive. abyss solves this problem by distributing the memory load over a given number of computer nodes in a computer cluster. minia [] implements a bloom filter data structure [] to represent a dbg stochastically in small memory and navigates it using a secondary data structure., in sequence assembly, there are several […]

PMCID: 4603742
PMID: 26451725
DOI: 10.1186/1471-2105-16-S14-S2

[…] for each of them, a set of simulated paired-end reads was generated with the tool wgsim ([]), with default parameters and a 20x mean covering depth. thereafter, assembly was performed with the tool minia ([]) with a k-mer size k = 29. reads were mapped on the contigs with bwa ([]), with default parameters and using the sampe method. the second dataset is composed of five scaffold graphs, […]

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Minia institution(s)
Computer Science department, ENS Cachan / IRISA / INRIA, Rennes, France; Algorizk, Paris, France
Minia funding source(s)
Supported with grant associated with the MAPPI project (ANR-10-COSI-0004) and the GATB project (ANR-12-EMMA-0019).

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