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Pipeline publication

[…] from a healthy control male mouse (C57BL/6) from the Institut Pasteur animal facility was collected, split, and processed through two meta3C protocols that solely differed by the restriction enzyme being used: either Hpa II [C′CGG] or Mlu CI [′AATT] ( and Materials and Methods). As discussed before (, ), using enzymes differing in the GC content of the corresponding restriction sites (RSs) is expected to improve contact coverage for GC- and AT-rich genomes. The Hpa II and Mlu CI libraries were sequenced on an Illumina NextSeq machine [2 × 75 base pairs (bp)], with 114 and 71 million PE reads recovered, respectively. Reads from both libraries were pooled and assembled into contigs using the IDBA-UD program (), resulting in 374,363 contigs (cumulated size, 580 Mb; N50, 3783 bp; maximum size, 490 kb; mean size, 1402 bp). Translated coding sequences resulting from this assembly [594,648 open reading frames (ORFs) detected—MetaGeneMark; ()] were analyzed at the taxon and functional levels using the metagenomics RAST (MG-RAST) pipeline (Materials and Methods) (). As expected from a gut metagenome, the major clades in the sample were Firmicutes (70%) and Bacteroidetes (15%) () (). An analysis of DNA sequences using the Kraken program () (Materials and Methods) confirmed these results with, also as expected, ~80% of the sequences not attributed to a specific genome (). Coding sequences were then annotated for essential genes, phages, and conjugative elements using repository databases (, , ), and the annotated contigs were then split into 1-kb fragments. This step has two objectives: first, to limit the impact of misassembly errors (such as chimeric contigs) arising during the assembly step, and second, to normalize the contact signal with respect to the influence of contig size on their representation during the segmentation of the network. Contigs under 500 bp were discarded, leading to a global set of 55 […]

Pipeline specifications

Software tools IDBA-UD, RAST, Kraken
Organisms Mus musculus, Homo sapiens