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This wiki contains some information on (NxTrim)(https://github.com/sequencing/NxTrim/wiki/Nextera-adapter-trimming), our software to process Nextera mate pairs.
We also give some more (general advice)(https://github.com/sequencing/NxTrim/wiki/Assembling-reads-from-a-mixture-of-Illumina-sample-preps) on the de-novo assembly of Illumina sequencing data, ranging from paired-end to synthetic long reads.