Computational protocol: Developing a Bacteroides System for Function-Based Screening of DNA from the Human Gut Microbiome

Similar protocols

Protocol publication

[…] Genome sequence data were generated on an Illumina MiSeq platform using 250-base paired-end sequencing. Sequence data were aligned to the B.¬†thetaiotaomicron VPI 5482 reference genome (NCBI accession no. NC_004663.1 for the chromosome and NC_004703.1 for the plasmid) using Bowtie 2 version 2.2.6 (). Sequence data were de novo assembled using SPAdes version 3.8.0 (), and functional annotations were obtained for contigs of interest using RAST (). Regions of similarity between host and clone DNA were identified using Mauve (). Data analyses were performed in R, including packages Rsamtools, Gviz, ape, and genoPlotR. […]

Pipeline specifications

Software tools Bowtie, SPAdes, RAST, Mauve, Rsamtools, genoPlotR
Applications Nucleotide sequence alignment, Genome data visualization
Organisms Homo sapiens, Escherichia coli, Bacteroides thetaiotaomicron