September 22, 2019  |  

MetaSort untangles metagenome assembly by reducing microbial community complexity.

Most current approaches to analyse metagenomic data rely on reference genomes. Novel microbial communities extend far beyond the coverage of reference databases and de novo metagenome assembly from complex microbial communities remains a great challenge. Here we present a novel experimental and bioinformatic framework, metaSort, for effective construction of bacterial genomes from metagenomic samples. MetaSort provides a sorted mini-metagenome approach based on flow cytometry and single-cell sequencing methodologies, and employs new computational algorithms to efficiently recover high-quality genomes from the sorted mini-metagenome by the complementary of the original metagenome. Through extensive evaluations, we demonstrated that metaSort has an excellent and unbiased performance on genome recovery and assembly. Furthermore, we applied metaSort to an unexplored microflora colonized on the surface of marine kelp and successfully recovered 75 high-quality genomes at one time. This approach will greatly improve access to microbial genomes from complex or novel communities.


September 22, 2019  |  

LSCplus: a fast solution for improving long read accuracy by short read alignment.

The single molecule, real time (SMRT) sequencing technology of Pacific Biosciences enables the acquisition of transcripts from end to end due to its ability to produce extraordinarily long reads (>10 kb). This new method of transcriptome sequencing has been applied to several projects on humans and model organisms. However, the raw data from SMRT sequencing are of relatively low quality, with a random error rate of approximately 15 %, for which error correction using next-generation sequencing (NGS) short reads is typically necessary. Few tools have been designed that apply a hybrid sequencing approach that combines NGS and SMRT data, and the most popular existing tool for error correction, LSC, has computing resource requirements that are too intensive for most laboratory and research groups. These shortcomings severely limit the application of SMRT long reads for transcriptome analysis.Here, we report an improved tool (LSCplus) for error correction with the LSC program as a reference. LSCplus overcomes the disadvantage of LSC’s time consumption and improves quality. Only 1/3-1/4 of the time and 1/20-1/25 of the error correction time is required using LSCplus compared with that required for using LSC.LSCplus is freely available at http://www.herbbol.org:8001/lscplus/ . Sample calculations are provided illustrating the precision and efficiency of this method regarding error correction and isoform detection.


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