Question: De-novo assembly using SPADES
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gravatar for ram.mainali
17 months ago by
ram.mainali10
ram.mainali10 wrote:

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

sequencing next-gen assembly • 1.1k views
ADD COMMENTlink modified 17 months ago by genomax65k • written 17 months ago by ram.mainali10

I tend to use the scaffolds.fasta file for subsequent steps of analysis as it should contain all scaffolded and non-scaffolded contigs. Quast command can be found here: http://quast.bioinf.spbau.ru/manual.html#sec2.1

ADD REPLYlink written 17 months ago by Sej Modha4.1k
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