Author: Sofia Morfopoulou; Vincent Plagnol
Title: Bayesian mixture analysis for metagenomic community profiling. Document date: 2014_7_25
ID: 058r9486_51
Snippet: The first step is the removal of clonal reads using an in house C++ script. We then use PRINSEQ (Schmieder and Edwards, 2011) for read-based quality control, removing low quality and complexity reads and performing 3'end trimming. For metagenomic analysis of human samples, reads originating from the human host are not relevant for our research question. We therefore remove human host reads, using a twostep approach to limit computation time: init.....
Document: The first step is the removal of clonal reads using an in house C++ script. We then use PRINSEQ (Schmieder and Edwards, 2011) for read-based quality control, removing low quality and complexity reads and performing 3'end trimming. For metagenomic analysis of human samples, reads originating from the human host are not relevant for our research question. We therefore remove human host reads, using a twostep approach to limit computation time: initially a short read aligner (novoalign, www.novocraft.com), followed by BLASTn. The next step is only applicable when the focus is on virus discovery using transcriptome reads. We remove ribosomal RNA sequences, using BLASTn against the Silva rRNA database (http://www.arb-silva.de/).
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