MITObim¶

Description¶

The pipeline was originally developed for Illumina data, but thanks to the versatility of the MIRA assembler, MITObim supports in principle also data from the Iontorrent, 454 and PacBio sequencing platforms.

Environment Modules¶

Run module spider mitobim to find out what environment modules are available for this application.

Environment Variables¶

HPC_MITOBIM_DIR - installation directory
HPC_MITOBIM_BIN - executable directory
HPC_MITOBIM_SCP - scripts directory
HPC_MITOBIM_EXE - example directory
HPC_MITOBIM_DOC - documentation directory

Citation¶

If you publish research that uses mitobim you have to cite it as follows:

Hahn, C., Bachmann, L., & Chevreux, B. (2013). Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—A baiting and iterative mapping approach. Nucleic Acids Research, 41(13), e129. https://doi.org/10.1093/nar/gkt371

Categories¶

phylogenetics