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  • #16
    No.

    @luc is referring to DISCOVAR DeNovo which is an assembler meant for large genomes. It *requires* 2 x 250 bp reads which currently can only be produced by suitably equipped HiSeq 2500 (in the amount needed, so MiSeq practically does not count).

    On a different note, DISCOVAR DeNovo also needs ~1 TB(+) of RAM to function well (e.g. you are going to use 500 million reads for assembly). You read that right!
    Last edited by GenoMax; 11-04-2015, 04:33 AM.

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    • #17
      The one time I tried out DISCOVAR DeNovo on a mammalian genome I had to borrow a 512 GB machine. As is all too typical for bioinformatics programs DISCOVAR at times took up all CPUs and at other times poked along using a single CPU. Relevant lines from the log file follow:

      Code:
      physical memory: 504.74 GB
      
      using 708,777,836 reads
      data extraction complete, peak mem = 260.85 GB
      3.27 hours used extracting reads
      
      back from buildReadQGraph
      memory in use = 191.83 GB, peak = 405.28 GB
      
      1 peak mem usage = 405.28 GB
      2.42 minutes used loading stuff
      2 peak mem usage = 405.28 GB
      launching gap assemblies, mem usage = 179,701,415,936
      
      now processing 411707 blobs
      memory in use = 191.38 GB, peak = 405.28 GB
      
      contig line N50: 46,487
      scaffold line N50: 108,870
      total bases in 1 kb+ scaffolds: 2,223,980,361
      total bases in 10 kb+ scaffolds: 2,102,334,133
      There are 708,777,836 reads of mean length 229.9 and mean base quality 34.3.
      MPL1 = mean length of first read in pair up to first error = 199
      (normal range is 175-225 for 250 base reads)
      Estimated chimera rate in read pairs (including mismapping) = 0.46%.
      genomic read coverage, using 1 kb+ scaffolds for genome size estimate: 73.3
      
      peak mem usage = 405.28 GB, total time = 40.9 hours
      Since I had mate-pairs I followed up DISCOVAR with BESST and got a very nice 2.4 GB genome with max of 9.7 MB, N50 of 1.8 MB with 375 scaffolds at N50 or greater.

      My "go-to" default assembler (ABySS) only came up with a 2.4 GB genome with max of 2.6 MB, N50 of 230 KB with 2,689 scaffolds at N50 or greater. So DISCOVAR/BESST is a nice option if you have the reads.

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      • #18
        Ok, sorry, I thought that reads needed to be 250 bp long in total not 2x250 bp. We cannot afford (and it has no sense) a HiSeq but we could purchase a NextSeq and try to perform deNovo (besides RNA-Seq and resec. but for that there is no problem).

        I work in a supercomputing center (but logically the sequencer will be used by a partner with background in genetics) so those computational requirements wouldn't be a problem. I'll have a look to DISCOVAR assembler.

        Thank you, best regards

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