Question: Abyss meta command line Inquiry
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4.9 years ago by
edge0 wrote:


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: abyss-pe np=60 k=25 name=soil lib='lib1 lib2 lib3 lib4 lib5' lib1='s1_1.fastq s1_2.fastq' lib2='s2_1.fastq s2_2.fastq' lib3='s3_1.fastq s3_2.fastq' lib4='s4_1.fastq s4_2.fastq' lib5='s5_1.fastq s5_2.fastq'

Can I know that is the above command correct if I wanna to run abyss meta? I'm not too sure how to specific the command to run abyss meta.

How to optimize my metagenomics assembly result? Is it I need to run at different mer etc? After then, choose the mer that given highest n50?

Thanks a lot and again for any advice.

abyss assembly • 1.2k views
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