Annotated bacterial chromosomes from frame-shift-corrected long-read metagenomic data

Microbiome

Sina Beier¹  Daniel H. Huson¹  Caner Bağcı¹  Anna Górska¹  Benjamin Buchfink²  Guanglei Qiu³  Krithika Arumugam³  Rohan B. H. Williams⁴  Irina Bessarab⁴ 

[1] Department of Computer Science, University of Tübingen, Sand 14;Max-Planck-Institute for Developmental Biology;Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University;Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore;

关键词: Microbiome;    Long-read sequencing;    Microbial genomics;    Sequence assembly;    Frame-shifts;    Algorithms;   

DOI  :  10.1186/s40168-019-0665-y

来源: DOAJ

【 摘 要 】

Abstract Background Short-read sequencing technologies have long been the work-horse of microbiome analysis. Continuing technological advances are making the application of long-read sequencing to metagenomic samples increasingly feasible. Results We demonstrate that whole bacterial chromosomes can be obtained from an enriched community, by application of MinION sequencing to a sample from an EBPR bioreactor, producing 6 Gb of sequence that assembles into multiple closed bacterial chromosomes. We provide a simple pipeline for processing such data, which includes a new approach to correcting erroneous frame-shifts. Conclusions Advances in long-read sequencing technology and corresponding algorithms will allow the routine extraction of whole chromosomes from environmental samples, providing a more detailed picture of individual members of a microbiome.

【 授权许可】

Unknown