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  • Bruno Vellutini 14:28 on 2014/06/19 Permalink
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    One more Membranipora 4D recording 


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    Started another recording at 1200. Animal pole view.

    File: BCV_Mm_2014_06_19 (old Mmem_19_06_14)

    Looks fine until 8 cell stage.

     
  • Bruno Vellutini 10:00 on 2014/06/19 Permalink
    Tags: , ,   

    Novocrania anomala genome 


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    Started a MaSuRCA assembly with Novocrania anomala paired ends only with the following config file:

    DATA
    PE= pe 300 15  /sysdev/s9/bruno/assemblies/Novocrania_anomala/data/Nano_pe_trimmed1.fastq.gz  /sysdev/s9/bruno/assemblies/Novocrania_anomala/data/Nano_pe_trimmed2.fastq.gz
    END
    
    PARAMETERS
    #this is k-mer size for deBruijn graph values between 25 and 101 are supported, auto will compute the optimal size based on the read data and GC content
    GRAPH_KMER_SIZE=auto
    #set this to 1 for Illumina-only assemblies and to 0 if you have 1x or more long (Sanger, 454) reads, you can also set this to 0 for large data sets with high jumping clone coverage, e.g. >50x
    USE_LINKING_MATES=1
    #this parameter is useful if you have too many jumping library mates. Typically set it to 60 for bacteria and something large (300) for mammals
    #LIMIT_JUMP_COVERAGE = 60
    #these are the additional parameters to Celera Assembler.  do not worry about performance, number or processors or batch sizes -- these are computed automatically. for mammals do not set cgwErrorRate above 0.15!!!
    CA_PARAMETERS = ovlMerSize=30 cgwErrorRate=0.25 ovlMemory=8GB ovlThreads=2
    #minimum count k-mers used in error correction 1 means all k-mers are used.  one can increase to 2 if coverage >100
    KMER_COUNT_THRESHOLD = 1
    #auto-detected number of cpus to use
    NUM_THREADS= 16
    #this is mandatory jellyfish hash size
    JF_SIZE=5000000000
    #this specifies if we do (1) or do not (0) want to trim long runs of homopolymers (e.g. GGGGGGGG) from 3' read ends, use it for high GC genomes
    DO_HOMOPOLYMER_TRIM=0
    END
     
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