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Protocol publication

[…] ey were included in specified analyses of the total cohort., Blood samples were drawn before surgery and plasma and serum samples were prepared and immediately frozen at −70 °C. The subjects were given material and instructions for providing fecal samples at home. Methods for processing fecal samples and isolation of metagenomic DNA have been described previously., All samples were sequenced in the Illumina HiSeq2000 instrument at SciLifeLab in Stockholm, Sweden, with up to ten samples pooled in one lane. Libraries were prepared with a fragment length of ~300 bp. Paired-end reads were generated with 100 bp in the forward and reverse direction., Sequencing adapter sequences were removed with cutadapt ( The length of each read was trimmed with SolexaQA with the options ‘-b –p 0.05’. Read pairs with either reads shorter than 35 bp were removed with a custom Python script. The high-quality reads were then aligned to the human genome (NCBI version 37) with Bowtie using ‘-n 2 -l 35 -e 200 –best -p 8 –chunkmbs 1024 -X 600 –tryhard’. This set of high-quality reads were then used for further analysis., A set of 2,382 microbial reference genomes were obtained from the NCBI and Human Microbiome Project on 02 August 2011. The reference genomes were combined into two Bowtie indexes and the metagenomic sequence reads were aligned to the reference genomes using Bowtie with parameters ‘-n 2 -l 35 -e 200 –best -p 8 –chunkmbs 1024 -X 600 –tryhard’. Mapping results were merged by selecting the alignment with fewest mismatches; if a read was aligned to a reference genome with the same number of mismatches, each genome was assigned half to each genome. The relative abundance of each genome was calculated by summing the number of reads aligned to that genome divided by the genome size. In each subject, the relative abundance was scaled to sum to one. The taxonomic rank for every genome was downloaded from NCBI taxonomy to assign each genome to a species, genus and phyla. The relative abundance for each taxonomical rank was calculated buy summing the relat […]

Pipeline specifications

Software tools cutadapt, SolexaQA, Bowtie
Databases HMP
Organisms Homo sapiens
Diseases Inflammation, Metabolic Diseases, Arterial Occlusive Diseases