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    Archive for June 1st, 2016

    Practical comparison of NGS adapter trimming tools

    1st June 2016

    I used to work with sequencing providers who were giving me fairly clean data.
    It was already barcode-separated, and had no over-represented adapter sequences.
    The only thing I had to do was to (optionally) quality-trim the reads, and check for biological contamination.

    Recently, however, I have come across some real-world data, which not only had contamination in it, but also quite a noticeable percentage of adapters.
    I did a quick test of multiple tools to see if they fit my requirements:

    • should be easy/logical to use: no arcane/convoluted command lines or config files
    • should detect adapters automatically, either using its own database or a provided plain FASTA file
    • should be reasonably fast
    • must leave no adapter traces behind: I prefer aggressive trimming

    I have tried the following tools:

    • fastq-mcf from the ea-tools package
    • skewer
    • TrimmomaticPE
    • cutadapt: haven’t used it directly, but it is used by some of the compared tools
    • bbduk from BBMAP
    • autoadapt
    • TrimGalore!

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    Posted in Bioinformatics | 6 Comments »