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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




No version available



  • person_outline Rayan Chikhi

Publication for Minia

Minia citations


Genomic repeats, misassembly and reannotation: a case study with long read resequencing of Porphyromonas gingivalis reference strains

BMC Genomics
PMCID: 5771137
PMID: 29338683
DOI: 10.1186/s12864-017-4429-4

[…] Genomics Workbench, and CodonCode Aligner); the others are freely available for academic purposes. Since de Bruijn graphs are inescapable (they are used by A5-miseq, CLC Genomics Workbench, Geneious, Minia, MIRA, SOAPdenovo2, SPAdes, and Velvet), we made an effort to also include different assembly methods, including Overlap-Layout-Consensus (CodonCode Aligner), string graph (fermi), and greedy al […]


Assembly and analysis of a qingke reference genome demonstrate its close genetic relation to modern cultivated barley

Plant Biotechnol J
PMCID: 5814578
PMID: 28871634
DOI: 10.1111/pbi.12826

[…] 5 paired‐end library, indicating that the peak frequency of K depth was about 21. Error correcting was undertaken using Allpaths‐lg's tools (Gnerre et al., ). De novo contig assembly was conducted by Minia v1.6906 (Chikhi and Rizk, ). SSPACE‐STANDARD‐3.0 (Boetzer et al., ) was used to link contigs into scaffolds with mate‐pair reads. Gaps in scaffolds_1 were filled using PBJelly 14.9.9 (English et […]


Allergen homologs in the Euroglyphus maynei draft genome

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

[…] eatMasker v1.317 [], SNAP [], and Augustus v3.0.1 []. SNAP utilized a scabies mite Hidden Markov Model (HMM) generated previously [] and Augustus used the BUSCO-generated model from the k = 47, m = 7 Minia assembly. Hints for gene predictions were based on 17,091 EST sequences from other Sarcoptiformes mites (NCBI EST database), and the CEGMA 458 core proteins []. Over 200 of the Maker predictions […]


Comparative scaffolding and gap filling of ancient bacterial genomes applied to two ancient Yersinia pestis genomes

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

[…] gaps characterized by Ns in the Ragout assembly. Also worth noting with the Marseille strain, MeDuSa was not able to correct a larger than expected contig assembly obtained with SPAdes. Finally, the Minia-AGapEs assemblies did not contain Ns due to the filling of the gaps uncovered by reads by the template sequence, we have indicated the length of template sequence used in parentheses instead. […]


Colib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads

PMCID: 4750246
PMID: 26870323
DOI: 10.1186/s13742-015-0105-2

[…] T, all the algorithms presented are based on an efficient representation of the de Bruijn graph with optimized bloom filters, implemented in the GATB C++ library [], as used for the first time in the MINIA [, ] assembler.A bloom filter is a probabilistic data structure that stores the presence/absence of items. It consists of a simple bit vector, initially all set to ‘0’. Any item is associated wi […]


Candidate pathogenicity islands in the genome of ‘Candidatus Rickettsiella isopodorum’, an intracellular bacterium infecting terrestrial isopod crustaceans

PMCID: 5181103
PMID: 28028472
DOI: 10.7717/peerj.2806

[…] atic v. 0.35 (), with a minimum leading and trailing sequence quality of 5, and a minimum internal sequence quality of 5 using a sliding window of 4 bp. An initial de novo assembly was performed with Minia 1.6906 (; ), with a k-mer size of 53 and a minimum k-mer depth of 4.Inspection of the resulting contigs revealed the presence of sequences from two distinct Rickettsiella-like endosymbionts. One […]

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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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