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  • An Extensive Evaluation of Read Trimming Effects on Illumina NGS Data Analysis

    Hi all,

    check this PLOS ONE paper out:
    An Extensive Evaluation of Read Trimming Effects on Illumina NGS Data Analysis
    Next Generation Sequencing is having an extremely strong impact in biological and medical research and diagnostics, with applications ranging from gene expression quantification to genotyping and genome reconstruction. Sequencing data is often provided as raw reads which are processed prior to analysis 1 of the most used preprocessing procedures is read trimming, which aims at removing low quality portions while preserving the longest high quality part of a NGS read. In the current work, we evaluate nine different trimming algorithms in four datasets and three common NGS-based applications (RNA-Seq, SNP calling and genome assembly). Trimming is shown to increase the quality and reliability of the analysis, with concurrent gains in terms of execution time and computational resources needed.


    Researchers from the Institute of Applied Genomics, Italy evaluated nine different trimming algorithms in four datasets and three common NGS-based applications (RNA-Seq, SNP calling and genome assembly). Trimming is shown to increase the quality and reliability of the analysis, with concurrent gains in terms of execution time and computational resources needed.

    The trimming tools investigated are:
    Cutadapt
    Condetri
    ERNE-filter
    FASTX
    prinseq
    Trimmomatic
    SolexaQA
    SolexaQA-bwa
    Sickle
    Last edited by peer.b; 01-08-2014, 05:57 AM. Reason: Fixing hyperlinks

  • #2
    Hi all,

    About this paper. Is it clearer to anyone why they claim that the window based tools are better for de novo assembly when at the same time they say these same tools (e.g. Trimmomatic and Sickle) give more fragmented assemblies (see N50 in Fig. 5)? I might being quite naif in the way I'm interpreting the results but except for the N50 I don't see any great differences in the two other parameter used to analyse assembly quality, and N50 seems to me to be worse in the window based tools..
    Fernando

    Comment


    • #3
      I disagree with the findings. They didn't even compare trimmed vs untrimmed in terms of misassemblies.

      Comment

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