Closed:Varying assembly statistics: Abyss & SPades
2
1
Entering edit mode
2.1 years ago
max_19 ▴ 150

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!

assembly abyss spades • 175 views
ADD COMMENT
This thread is not open. No new answers may be added
Traffic: 1520 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6