Mimeo
Table of contents
Modules
Mimeo comprises three tools for parsing repeats from whole-genome alignments:
mimeo-self
Internal repeat finder. Mimeo-self aligns a genome to itself and extracts high-identity segments above a coverage threshold. This method is less sensitive to disruption by indels and repeat-directed point mutations than kmer-based methods such as RepeatScout. Reported annotations indicate overlapping segments above the coverage threshold, mimeo-self does not attempt to separate nested repeats. Use this tool to identify candidate repeat regions for curated annotation.
mimeo-x
Cross-species repeat finder. A newly acquired or low-copy transposon may slip past copy-number based annotation tools. Mimeo-x searches for features which are abundant in an external reference genome, allowing for annotation of complete elements as they occur in a horizontal-transfer donor species, or of conserved coding segments of related transposon families.
mimeo-map
Find all high-identity segments shared between genomes. Mimeo-map identifies candidate horizontally transferred segments between sufficiently diverged species. When comparing isolates of a single species, aligned segments correspond to directly homologous sequences and internally repetitive features.
Intra/Inter-genomic alignments from Mimeo-self or Mimeo-x can be reprocessed with Mimeo-map to generate annotations of unfiltered/uncollapsed alignments. These raw alignment annotations can be used to interrogate repetitive-segments for coverage breakpoints corresponding to nested transposons with differing abundances across the genome.
mimeo-filter
An additional tool mimeo-filter is now included to allow post-filtering of SSR-rich sequences from FASTA formatted candidate-repeat libraries.
Installing Mimeo
Requirements:
Install from Bioconda:
Install from PyPi:
Clone and install from this repository:
License
Software provided under MIT license.