Before, I used SOAPdenovo2 to assemble my target reads. In order to use multiple k-mer and have better assembly result, I used SPADES for de-novo assembly using following commands
SPAdes-3.9.1-Linux/bin/spades.py -1 insert_seq.JV18.k19_R1.fq -2 insert_seq.JV18.k19_R2.fq -t 2 -m 100 -o spades.JV18 --phred-offset 33
It produced two separate assembly result for scaffolded contig and unscaffolded contig. My question is how can I merge these two type of contig (because I need to use them as reference for alignment later).
I produced the result and evaluated the assembly characteristics by using Perl assemblathon_stats.pl with input contigs.fasta and scaffolds.fasta separately. I the oubt on relevance of using this perl script for assembly result of SPADES. The manual suggests oN using QUAST (http://bioinf.spbau.ru/en/quast). Could you please suggest me command for QUAST run. What is your perception regarding use of these two type of assembly?
I am a beginner in this field. Any suggestions are highly welcomed. thank you