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Fig. 1 | Microbiome

Fig. 1

From: Transductomics: sequencing-based detection and analysis of transduced DNA in pure cultures and microbial communities

Fig. 1

The “transductomics” workflow. In the sample preparation step, the sample is gently homogenized and split into two subsamples. One subsample is directly used for whole community DNA extraction, the other subsample is subjected to ultra-purification of virus-like particles (VLPs) using a combination of filtration, DNAse digestion, and CsCl density gradient centrifugation as previously described [24] followed by DNA extraction from the purified VLPs. Both DNA samples are sequenced to different depths and potentially with different sequencing approaches, although in many cases the same sequencing approach could be applied to both samples. For the whole community DNA sample, the sequencing must focus on ultimately achieving assembly of long metagenomic contigs. For the VLP DNA sample, the sequencing must focus on maximal read coverage, and no assembly is needed for these reads. The whole community sequencing reads are assembled using a suitable assembler. Contigs smaller than 40 kbp are discarded. Both the whole community and VLP sequencing reads are mapped onto the contigs > 40 kbp using BBMap [25] ensuring that ambiguously mapped reads are only used once and randomly assigned. To find transduced regions, the contig read coverage patterns for both whole community and VLP reads are visualized using the Integrative Genomics Viewer [26]

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