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

BMC Bioinformatics

Software

Thomas Nordahl Petersen¹  Thomas Sicheritz-Pontén¹  Kosai Al-Nakeeb¹ 

[1] Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, Building 208, 2800, Kgs Lyngby, Denmark;

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

DOI  :  10.1186/s12859-017-1927-y

 received in 2017-05-22, accepted in 2017-11-06,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundWhole-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.ResultsNorgal (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.ConclusionNorgal 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】

CC BY   
© The Author(s) 2017