Similar protocols

Pipeline publication

[…] aries were created from 5 μg of total DNA for each sample. The resulting read length was 50 bp., The analysis of the raw metagenomic reads included quality preprocessing followed by the identification of taxonomic and functional composition (semiquantitative profiling of the abundance of the microbial taxa and functional gene groups, respectively). These analyses were performed as described before [, ], with the modification of the references. The reference sets included a nonredundant set of 353 gut microbial genomes (for the taxonomic analysis) [] and a gut microbial gene catalogue of 9.9 mln genes (for the functional analysis) []., As an additional method for taxonomic profiling, we used MetaPhlAn v2.0 software based on the identification of unique clade-specific genetic sequences []. The read alignment step of MetaPhlAn was performed using Bowtie []. For the MetaFast analysis [], the color-space SOLiD metagenomic reads of the patients and control group were subjected to human sequences filtering, error correction using SAET, and conversion to base-space format. The MetaFast was used with the default settings. The metagenomes were hierarchically clustered using the dissimilarity matrix; the outliers were defined as the metagenomes belonging to the smaller branch after cutting the clustering tree at the top level., The KEGG metabolic pathways differentially abundant between two groups of metagenomes were identified using piano R [] package (parameters: gene set analysis using “reporter feature algorithm,” significance assessment using “gene sampli […]

Pipeline specifications

Software tools MetaPhlAn, Bowtie, MetaFast