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  • SPAdes assembler

    Hello,
    I tried to assemble a mitochondrial genome assembly with SPAdes assembler using pair-end Illumina and Nanopore sequencing data. The size of the Illumina data is 18 GB and when I do hybrid assembly after trimming adapters, it showing that Memory is insufficient to run this program and requires at least 389 GB RAM. But, I am having 188 GB RAM.
    Then, I used BBmerge commands to sort out this issue. But when I run pair-end reads using bbmerge-auto.sh command, its saying that "try increasing the -Xmx flag and using tool specific memory related parameters".

    Please suggest me how to do hybrid assembly with both Illumina and Nanopore data?

  • #2
    Is your 18 Gb of Illumina data pure mtDNA or mtDNA plus nuclear? If it is pure mtDNA then you probably have many thousand-fold coverage of the mitochondrial genome and you can reduce the number of reads used as input (bbtools reformat will do that if you give the paired-end reads as in= and in2= and then use reads=10000000 or some other number). If it is not pure mtDNA then you probably still have high coverage and could cut the input by 3/4s.
    Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

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    • #3
      Thank you so much for your kind reply.

      Its whole genomic data that includes, chloroplast, mitochondrial and nuclear genome data. How can I choose 3/4 read? Could you please suggest.

      Thank you so much.

      With warm regards,
      Raman. G

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      • #4
        I would use bbtools reformat to set the number of desired reads.
        Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

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        • #5
          Could you please give me with some examples. I am new to bioinformatics. How to set desired reads...

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          • #6
            You used bbmerge already, so it sounds like you have bbtools installed.
            reformat.sh in=read1,fq,gz in2=read2.fq.gz out=read1_fewer.fq.gz out2=read2_fewer.fq.gz reads=10000000
            Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

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            • #7
              Thank you so much.

              by the way, I have used this command to estimate genome size using the following command:
              java -ea -Xmx188g -Xms188g -cp /home/pmslab/Desktop/Raman/bin/bin/bbmap/current/ jgi.KmerCountExact in=trim_CKEMJ1.fastq in2=trim_CKEMJ2.fastq khist=khist_trim_CKEMJ.txt peaks=peaks_trim_CKEMJ.txt -Xmx188g

              But i got an error message:
              ./../bin/bin/bbmap/kmercountexact.sh: line 138: 30199 Killed

              What could be the problem?
              Thank you.

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