SqueezeMeta, A Highly Portable, Fully Automatic Metagenomic Analysis Pipeline.

摘要: The improvement of sequencing technologies has facilitated generalization metagenomic sequencing, which become a standard procedure for analyzing the structure and functionality microbiomes. Bioinformatic analysis results poses challenge because it involves many different complex steps. SqueezeMeta is fully automatic pipeline metagenomics/metatranscriptomics, covering all steps analysis. includes multi-metagenome support that enables co-assembly related metagenomes retrieval individual genomes via binning procedures. features several unique characteristics: or unlimited number merging assembled metagenomes, both with read mapping estimation abundances genes in each metagenome. It also bin checking retrieving genomes. Internal checks assembly provide information about consistency contigs bins. Moreover, are stored MySQL database, where they can be easily exported shared, inspected anywhere using flexible web interface allows simple creation queries. We illustrate potential by 32 gut way, enabling million hundreds genomic One motivations development was producing software capable running small desktop computers thus amenable to users settings. were able co-assemble two these complete full less than one day laptop computer. This reveals capacity run without high-performance computing infrastructure absence any network connectivity. therefore adequate situ, real time produced nanopore sequencing. downloaded from https://github.com/jtamames/SqueezeMeta.