Recent content by cjfields

  1. C

    Human metagenomic data, two-stage or one-stage approach?

    I highly recommend two-stage, filtering host reads prior to metagenome analysis. We have used Huttenhower's kneadData for this which can align reads for you and split into 'contaminated' and 'clean' bins, but you may want to use an alternative two-stage approach (e.g. alternate aligner like bwa...