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

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

Kosai Al-Nakeeb, Thomas Nordahl Petersen, Thomas Sicheritz-Pontén

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 were able to extract full circular mitochondrial genomes and obtained sequence identities to the reference sequences in the range from 98.5 to 99.5%. We also assembled the chloroplasts of grape vines and cucumbers using Norgal together with seed-based de novo assemblers. Conclusion Norgal is a pipeline that can extract and assemble full or partial mitochondrial and chloroplast genomes from WGS short reads without prior knowledge. The program is available at: https://bitbucket.org/kosaidtu/norgal .

2017

mitochondrial DNA, k-mer, Next-generation sequencing, de novo assembly

DOI: 10.1186/s12859-017-1927-y

BMC Bioinformatics

BMC

Biology (General), Computer applications to medicine. Medical informatics

EN