Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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

    Comment


    • #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

      Comment


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

        Comment


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

          Comment


          • #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

            Comment


            • #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.

              Comment

              Latest Articles

              Collapse

              • seqadmin
                Strategies for Sequencing Challenging Samples
                by seqadmin


                Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
                03-22-2024, 06:39 AM
              • seqadmin
                Techniques and Challenges in Conservation Genomics
                by seqadmin



                The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

                Avian Conservation
                Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
                03-08-2024, 10:41 AM

              ad_right_rmr

              Collapse

              News

              Collapse

              Topics Statistics Last Post
              Started by seqadmin, 03-27-2024, 06:37 PM
              0 responses
              15 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 03-27-2024, 06:07 PM
              0 responses
              13 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 03-22-2024, 10:03 AM
              0 responses
              55 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 03-21-2024, 07:32 AM
              0 responses
              70 views
              0 likes
              Last Post seqadmin  
              Working...
              X