Recently, I have got my NGS results for 5 bacterial samples; 5 files for each sample (R1.fasatq, R2.fastaq and SNP indel excel file). I tried using HGTector tool ( Article HGTector: An automated method facilitating genome-wide disco... ), but to be capable of using this tool, I have to identify all the coding regions in the genome and translate it into proteins. That's why I started using denovo genome assembly tools. ABySS tool was used by implementing this command. [ sudo abyss-pe name=25.3.2019karam_S-1 k=64 in='Karam_S_1.fastq Karam_S_2.fastq' ] and the output files are provided in the picture. I have recognized that all the fasta files included more than one contig, so how I can assemble all the contigs into one circular DNA (I need the full genome not the reads)?. I have tried using chromaspro software,

I have tried using chromaspro software to assemble the resulted contigs into larger fragments, but it seems that it requires a large RAM. I think that I need to search for other tools.

Note: I am trying to find a Horizontal gene transfer event between two bacteria, as I have observed an abnormal phenotype in the experiment I was working on.