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Old 02-08-2020, 05:45 PM   #1
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Location: South Korea

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Default SPAdes assembler

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 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?
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Old 02-09-2020, 08:28 PM   #2
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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.
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