Hi, I'm having 5 metagenomics soil sample from different areas. It is sequenced by using Illumina pair-end, 2 X 101 nt, 1GB file size for each sample, insert size is 300 - 400 nt. The objective of this research is to determine and compare the spectrum of microbiodata of the soil sources in different areas.
I have done the standard pre-processing step (trim adaptor, remove duplicate read, remove low quality read, etc). I got 5 sets of clean read (proper pair-end but variable length due to trim process) metagenomics soil sample now. Below is the command I try: *mpiexec -n 60 Ray -k 31 -p s1_1.fastq s1_2.fastq -p s2_1.fastq s2_2.fastq -p s3_1.fastq s3_2.fastq -p s4_1.fastq s4_2.fastq -p s5_1.fastq s5_2.fastq -o Soil_Metagenomics* Can I know that is the above command correct if I wanna to run Ray meta? I'm not too sure how to specific the command to run Ray meta. How to optimize my metagenomics assembly result? Is it I need to run at different mer etc? Once I get the Thanks a lot and again for your advice.
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