http:\/\/4dgeo.whoi.edu\/jason\/<\/a>).<\/p>\nDNA extraction: <\/strong>Total genomic DNA (gDNA) was extracted from each sample in duplicate using the FastDNA Spin Kit for Soil following the manufacturer's protocol (Qbiogene, Irvine, CA). Extracted gDNA from each sample was pooled, cleaned, and concentrated using Mont\u00e1ge PCR centrifugal filter devices (Millipore, Bedford, MA). The gDNAs were then quantified using a Nanodrop ND-1000 spectrophotometer and were diluted to 10 ng DNA\/ml using filter sterilized 10 mM Tris 0.1 mM EDTA (pH 8.0).<\/p>\nMetagenome sequencing: <\/strong>Two micrograms of gDNA was sheared using a Covaris S2 sonicator and 400bp fragments were size selected for library construction. The library was constructed using the TruSeq DNA sample prep kit (Illumina) following the manufactures protocol. Sequencing was performed using an Illumina HiSeq 2000 sequencer.<\/p><\/div>","@type":"rdf:HTML"}],"http:\/\/ocean-data.org\/schema\/hasBriefDescription":[{"@value":"Metegenomic sequences from Lau Basin low temperature vents and Loihi Seamount.","@language":"en-US"}],"http:\/\/purl.org\/dc\/terms\/description":[{"@value":"Metegenomic sequences from Lau Basin low temperature vents and Loihi Seamount; collected on the 2012 \"Submarine Ring of Fire\" (SRoF) cruise and the 2008 FeMO cruise.<\/p><\/div>","@type":"rdf:HTML"}],"http:\/\/www.w3.org\/2000\/01\/rdf-schema#label":[{"@value":"Lau Basin and Loihi Seamount microbial mats","@type":"xsd:string"}],"http:\/\/ocean-data.org\/schema\/hasProcessingDescription":[{"@value":"
Metagenome quality control and assembly:<\/strong> Sequences were quality controlled and trimmed using the program Sickle. The trimmed sequences were then digitally normalized using the program Khmer utilizing a two-pass strategy. The sequences were first normalized by median to reduce sequences with high-abundance kmers using a kmer size of 20bp and a maximum coverage overlap value of 20. The sequences were then filtered to remove low-abundance kmers and Illumina sequencing artifacts using the Khmer script filter-below-abund with a minimum overlap of 2 kmers. The remaining sequences after preprocessing were used for sequence assembly.<\/p>\nThe normalized reads were assembled using the de Bruijn graph-based assembler Velvet. Four independent assemblies were constructed with kmer sizes of 41, 51, 61, and 71. The contigs were assembled into \"supercontigs\"\u00a0using the program Geneious with a minimum overlap of 25bp. Contigs longer than 1000bp were exported and used in further analysis.<\/p>\n
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