Comprehensive Metagenomic Sequencing Workflow

An overview of the samples and methodology used in this study is provided in Figure 1. Sample collection, DNA extraction, random fragmentation and cloning of approximately 3-kb fragments, Sanger sequencing, assembly, and curation of community genomics data were performed using phred/phrap/consed package as detailed previously [12 (link),55 (link)]. The combined UBAs nonLeptos dataset was constructed by assembling sequencing reads derived from both the UBA BS and UBA biofilm samples (with UBA reads previously assigned to Leptospirillum spp. removed). This included 229,082 reads and approximately 210 Mb of total sequence, which assembled into 15,929 contigs and 36.6 Mb of composite sequence.

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Dick G.J., Andersson A.F., Baker B.J., Simmons S.L., Thomas B.C., Yelton A.P, & Banfield J.F. (2009). Community-wide analysis of microbial genome sequence signatures. Genome Biology, 10(8), R85.

Publication 2009

Biofilm Sample collection

Corresponding Organization :

Other organizations : University of Michigan–Ann Arbor, Planetary Science Institute, University of California, Berkeley, Uppsala University

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Protocol cited in 36 other protocols

Variable analysis

independent variables

Sample collection
DNA extraction
Random fragmentation and cloning of approximately 3-kb fragments
Sanger sequencing

dependent variables

Assembly of sequencing reads
Curation of community genomics data

control variables

Phred/phrap/consed package used for assembly and curation, as detailed in previous studies [12, 55]

controls

No positive or negative controls were explicitly mentioned in the provided information.

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