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

BMC Bioinformatics

Thomas Nordahl Petersen¹  Kosai Al-Nakeeb¹  Thomas Sicheritz-Pontén¹ 

[1] Department of Bio and Health Informatics, Technical University of Denmark;

关键词: Mitochondrial dna;    K-mer;    Next-generation sequencing;    De novo assembly;   

DOI  :  10.1186/s12859-017-1927-y

来源: DOAJ

【 摘 要 】

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 .

【 授权许可】

Unknown