MITObim pipeline

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
Requirements GNU utilities, MIRA
Maintained Yes



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  • person_outline Christoph Hahn <>

Publication for MITOchondrial Baiting and Iterative Mapping

MITObim IN pipelines

PMCID: 5805877
PMID: 29439039
DOI: 10.1128/genomeA.01395-17

[…] whole-genome sequencing was conducted using the illumina hiseq 4000 platform at hangzhou lianchuan biotechnology co., ltd. (hangzhou, china). quality-controlled trimmed reads were assembled with mitobim version 1.8 software. the coverage was on the order of 1,000×, and one contig was obtained. potential open reading frames (orfs) were identified with genemarks version 4.17 (6), […]

PMCID: 5662180
PMID: 29084259
DOI: 10.1371/journal.pone.0187316

[…] quality of the data was performed using trimmomatic v0.33 [23] with the following settings: sliding window 4:20. minimum read length:100. mitogenomes were reconstructed by iterative mapping using mitobim v1.8 [24]. the complete mitogenome of corvus splendens was used as reference in the mapping., duplications in the region between the cytb gene and the 12s rrna gene have frequently […]

PMCID: 4839110
PMID: 27103937
DOI: 10.1186/s12983-016-0150-4

[…] sequencing depth. here only genus and family level identifications were considered., mitochondrial genomes of p. f. femoralis were obtained by metagenomic assembly on one samples (blm5) using mitobim [49] under default parameters and the mitochondrial genome of the related p. melalophos (genbank: nc_008217) as reference. the genome was annotated using mitos [50] and further manually […]

PMCID: 4982428
PMID: 27514512
DOI: 10.1186/s12879-016-1731-8

[…] miseq sequencer located at the monash university malaysia genomics facility (run configuration of 2 × 150 bps paired-end read). reference mapping to the complete genome of denv was performed using mitobim version 1.8 (default setting) [21]. the assembled genomes of 6 denv-2 and 5 denv-1 (denv-2: tm26, tm78, tm181, tm198, tm213, tm296; denv-1: tm24, tm50, tm99, tm100, tm242) along […]

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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