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MITObim specifications


Unique identifier OMICS_13338
Name MITObim
Alternative name MITOchondrial Baiting and Iterative Mapping
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages Perl, Python
License MIT License
Computer skills Advanced
Version 1.8
Stability Stable
GNU utilities, MIRA
Maintained Yes




No version available



  • person_outline Christoph Hahn

Publication for MITOchondrial Baiting and Iterative Mapping

MITObim citations


Complete mitochondrial and rDNA complex sequences of important vector species of Biomphalaria, obligatory hosts of the human infecting blood fluke, Schistosoma mansoni

Sci Rep
PMCID: 5943310
PMID: 29743617
DOI: 10.1038/s41598-018-25463-z
call_split See protocol

[…] Two methods were used to assemble mitochondrial genomes, the semi-reference based assembly using MITOBIM and de novo assembly using SPAdes. MITOBIM is a tool developed to recursively find reads mapped to related reference mitogenomes and uses these reads to build the targeted mitogenome. The publ […]


New insights into the phylogenetics and population structure of the prairie falcon (Falco mexicanus)

BMC Genomics
PMCID: 5885362
PMID: 29618317
DOI: 10.1186/s12864-018-4615-z

[…] We used baiting and iterative mapping in MITObim 1.6 [] to create an initial draft of the mitochondrial genome, using a F. mexicanus COI (cytochrome c oxidase subunit I) barcode sequence (AY666553) to initiate assembly. As a quality control […]


Phylogenomics and barcoding of Panax: toward the identification of ginseng species

BMC Evol Biol
PMCID: 5883351
PMID: 29614961
DOI: 10.1186/s12862-018-1160-y
call_split See protocol

[…] filtering of reads using a sliding window of 15 bp and an average Phred threshold of 20. Low-end quality bases below a Phred score of 20 were removed, and only reads longer than 100 bp were retained. MITOBim version 1.7 [] was used for assembly of the single-end Ion Torrent reads using iterative mapping with in silico baiting using the following reference plastomes, P. vietnamensis (KP036470) and […]


A new strategy to infer circularity applied to four new complete frog mitogenomes

Ecol Evol
PMCID: 5916287
PMID: 29721275
DOI: 10.1002/ece3.3918

[…] , Peplies, & Glöckner, ), among other applications. In the context of finding circular sequences via k‐mer matching, however, the software that is most similar to AWA is (distributed with MITObim).The program takes a sequence in FASTA format and some parameters such as k‐mer size, expected sequence length, and a value of tolerance for length variation. The algorithm proceed […]


Comparative Chloroplast Genomics of Gossypium Species: Insights Into Repeat Sequence Variations and Phylogeny

Front Plant Sci
PMCID: 5871733
PMID: 29619041
DOI: 10.3389/fpls.2018.00376

[…] , China). The raw reads obtained were quality trimmed using the program NGSQCtoolkit v2.3.3 (). We used the reference-guided assembly method to reconstruct the plastid genomes with MIRA v4.0.2 () and MITObim-master (). In this analysis, we used the chloroplast genome of the closely related species G. hirsutum (AD1) (NC_007944) as the reference sequence. In addition, four small gaps and ambiguous s […]


Molecular Evolution of Chloroplast Genomes of Orchid Species: Insights into Phylogenetic Relationship and Adaptive Evolution

Int J Mol Sci
PMCID: 5877577
PMID: 29498674
DOI: 10.3390/ijms19030716
call_split See protocol

[…] First, we used the software, NGSQCToolkit v2.3.3 [], to trim the low-quality reads. After removing the low-quality sequences, the clean reads were assembled using MIRA v4.0.2 [] and MITObim v1.8 [] with the cp genome of a closely-related species, Dendrobium nobile (KX377961), as reference. The programs, DOGMA ( [] and Geneious v8.0.2 [] were used to […]


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MITObim institution(s)
Natural History Museum, University of Oslo, Oslo, Norway; Department for Human Nutrition and Health, DSM Nutritional Products Ltd, Kaiseraugst, Switzerland
MITObim funding source(s)
This work was supported by Internal funding of the Natural History Museum, University of Oslo, Norway.

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