Possibilities of Reassembly too many metagenomic NGS-assembled short contigs

[neptuneyt]

Dear megahit team, Thanks for your so excellent work first of all. I have 200 Illumina paired-end 150 bp metagenomic sequence samples. I used megahit to assemble each sample very fast but result to many short contigs 500bp-3000 bp (accounting for > 90% of the total assembly contig numbers).

• Q: so I wonder is there possibility to reassemble these short contigs (or combined with longer than 3k long contigs) to scafflods? which toolkit/software do you recommand? command:

  time megahit -t 100 --min-contig-len 500 --out-dir ./ -1 A_1.fq.gz -2 A_2.fq.gz &>log 

  Thank you from the bottom of my heart! Looking forward your reply!