Closed:Varying assembly statistics: Abyss & SPades

Question

[max_19]

Hi guys!

I am trying to assemble a genome of ~5MB and I have 250bp PE reads. I tried assembling with Abyss:

abyss-pe k=64 name=novo in='r1.fastq r2.fastq'

This resulted in a scaffold N50 of 50k and total assembly size of 5MB (and if you run with k=128, N50=60k and total assembly size=4.5MB). I wanted to see if I can improve this using SPades so I ran it like this:

spades.py -1 r1.fastq -2 r2.fastq --careful -k 21,33,55,77,99,127 -o spades_assembly

And then used QUAST to get assembly stats like so:

quast-5.0.2/quast.py scaffolds.fasta -o report

The surprising result is that the resulting stats are a lot worse (low N50 of 1455, very high total length of 18 million) and I have to think that something went wrong or maybe I am missing something. --careful flag runs error correcting which is not done in Abyss but I don't think this is the reason? Full output of QUAST is below:

Assembly                    scaffolds
# contigs (>= 0 bp)         32842    
# contigs (>= 1000 bp)      2918     
# contigs (>= 5000 bp)      170      
# contigs (>= 10000 bp)     85       
# contigs (>= 25000 bp)     50       
# contigs (>= 50000 bp)     34       
Total length (>= 0 bp)      25940092 
Total length (>= 1000 bp)   11070707 
Total length (>= 5000 bp)   6648867  
Total length (>= 10000 bp)  6094453  
Total length (>= 25000 bp)  5557460  
Total length (>= 50000 bp)  4920491  
# contigs                   14063    
Largest contig              446405   
Total length                18374693 
GC (%)                      42.66    
N50                         1455     
N75                         708      
L50                         1327     
L75                         6199     
# N's per 100 kbp           84.79

Thanks for any input!