MetaSpades Paired, Unpaired, and Single-End Reads

[SalJahromi]

Hello,

I am currently working on a metagenomics project with Spades. After QC, there are two types of samples:

1. Samples with paired forward and reverse, and unpaired forward and reverse (4 files)
2. Samples with single-end reads.

For the first type, I ran it like shown below and it worked.

        metaspades.py \
        --pe1-1 $forward_paired_file \
        --pe1-2 $reverse_paired_file \
        --pe1-s $forward_unpaired_file \
        --pe1-s $reverse_unpaired_file \
        -o "metaspades_outputs_try2/$folder_name"

I'm now wondering if there is a way to run the single-end samples with pe-s parameter in metaspades. I tired giving the file as an input twice, which did not work.

Thanks