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Using Deconseq

    Deconseq is installed in my (gribskov) local directory or in the bioinformatics modules.  If you use the versions in the bioinformatics modules you will have to do some configuration and either download or create some databases.  

    Bioinformatics module version

    • module load deconseq
    • module show deconseq
    • see the README for mote information (currently /apps/group/bioinformatics/apps/deconseq-standalone-0.4.3/README)

    Gribskov version

    If you are in the mgribsko group you should have access to my version, which includes libraries designed for plant transciptomes.

    • the deconseq executable is located in /home/mgribsko/deconseq.  This includes
      • deconseq.pl - the deconseq script
      • DeconSeqConfig.pm - the perl module that defines the databases and other essentials
      • bwa64 - the particular version of BWA used by Deconseq
      • /home/mgribsko/deconseq/db - the libraries I made (spring 2012)
        • bactera - all complete bacterial genomes
        • virus - all complete viral genomes
        • chloroplast - all complete chloroplast genomes
        • mitochondrion - all complete mitochondrial genomes
        • rna - ribosomal RNA sequences augmented with additional P. vittata rRNA
    • I usually run deconseq using a script, either /home/mgribsko/NGS/clean_deconseq.pl or /home/mgribsko/NGS/clean_deconseq_parallel.pl.  The latter script allows you 
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