Can I assemble the paired-end and single-end sequences separately and then use staramr to obtain their ARGs information together? This is because my fastq files contain both paired-end and single-end sequences.
Hi @Sanji
You can assemble all of the reads together using → SPAdes genome assembler for genomes of regular and single-cell projects
The tool form has options for additional reads. Pleaes give that a review and let us know if it solves your question. Thanks!
I used MEGAHIT, is it OK?
Hi @Sanji
You can try any of the assembly tools that you want to. 
The other has some tutorials as well – see the bottom of the tool form for links.
I have a question I’d like to ask you. I used Trimmomatic for trimming and then checked the quality with MultiQC. I found that the Per Base Sequence Content, Per Sequence GC Content, Sequence Duplication Levels, and Overrepresented Sequences were red, while the Sequence Length Distribution was orange, and the rest were green. I plan to assemble the data to retrieve ARGs information next. Are there any steps I need to take to prevent these metrics from turning red? Will the current quality check results significantly impact my subsequent analysis?
Yes, assembly is sensitive to the input read quality.
For QA tutorials, including discussion about how to interpret FastQC/MultiQC results, please see the tutorials here → GTN Materials Search. Start with this one → Hands-on: Quality Control / Sequence analysis. Our Assembly tutorials have more, please see → Assembly / Tutorial List