Norgal: extraction and de novo assembly of mitochondrial DNA from whole-genome sequencing data.

ABSTRACT:

Background

Whole-genome sequencing (WGS) projects provide short read nucleotide sequences from nuclear and possibly organelle DNA depending on the source of origin. Mitochondrial DNA is present in animals and fungi, while plants contain DNA from both mitochondria and chloroplasts. Current techniques for separating organelle reads from nuclear reads in WGS data require full reference or partial seed sequences for assembling.

Results

Norgal (de Novo ORGAneLle extractor) avoids this requirement by identifying a high frequency subset of k-mers that are predominantly of mitochondrial origin and performing a de novo assembly on a subset of reads that contains these k-mers. The method was applied to WGS data from a panda, brown algae seaweed, butterfly and filamentous fungus. We we

SUBMITTER: Al-Nakeeb K 

PROVIDER: S-EPMC5699183 | biostudies-literature | 2017 Nov

REPOSITORIES: biostudies-literature