“Simplifing” a very fragmented genome for visualisation?

“Simplifing” a very fragmented genome for visualisation?

1

Hi there,

I have a very fragmented reference genome that i want to visualize (with jbrowse or similar)

this is the paper for the genome: link

here the genome can be found: link2

here are the quast statistics:

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QUAST Results
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All statistics are based on contigs of size >= 500 bp, unless otherwise noted (e.g., "# contigs (>= 0 bp)" and "Total length (>= 0 bp)" include all contigs).

Assembly                    Abal.1_1   
# contigs (>= 0 bp)         37192295   
# contigs (>= 1000 bp)      1276678    
# contigs (>= 5000 bp)      529013     
# contigs (>= 10000 bp)     343016     
# contigs (>= 25000 bp)     145508     
# contigs (>= 50000 bp)     46234      
Total length (>= 0 bp)      18167382048
Total length (>= 1000 bp)   13017811908
Total length (>= 5000 bp)   11361640463
Total length (>= 10000 bp)  10034318481
Total length (>= 25000 bp)  6872368770 
Total length (>= 50000 bp)  3406852776 
# contigs                   1887964    
Largest contig              297427     
Total length                13450974050
GC (%)                      38.76      
N50                         25814      
N75                         9780       
L50                         139726     
L75                         348468     
# N's per 100 kbp           1703.76  

any help how i can wrangle this beast into something presentable would be helpful.

I tried a cutoff to get rid of the contigs < 1000bp wich helped, but is there a way to rescaffold or similar?


fasta


reference


visualisation


genome

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