fasta index file too big for genome browsers

Question

[setschmann]

Hi,

I have a very fragmented reference genome https://www.g3journal.org/content/9/7/2039 samtool generate a huge fai index file of 1.35gb, which is way too big to load into Jbrowse2.

How can i "simplify" the fasta or the fai file? what tools could i use?

[samuel.a.odonnell]

You could try scaffolding if it has a close relative with a more contiguous assembly. Would help reduce the number of contigs

[Ram]

The index file is 1.35G? That seems really odd. What was the exact command you used to generate the index?

[setschmann]

samtools faidx name.fa

the problem is the genome is very fragemented:

those are the quast results:

########
QUAST Results
########

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  

[Ram]

From Istvan's reply and yours, it looks like you're doing things right. Like he says, a graphical tool might not work best for your requirement. See if you can either work with a different tool or tweak your requirement.

[setschmann]

il try to remove contigs with less than 1000bp and see how it goes

[Ram]

That's still a million contigs. Genome Browsers are built to deal with contigs that number in the 10s (<50) typically. I hope this subset works out for you.

Answer 1

[Istvan Albert]

One might say that there is no point in loading a genome with 37 million contigs into a browser, many of the expected GUI widgets would be inoperable,

for example, the graphical dropdown widget to select chromosomes would now have 37 million entries ...

instead, select a few dozen of interesting contigs where it would make sense to look at the genome and visualize those.

[setschmann]

okay, but i would need to import it as a reference genome, a few contigs wouldnt be enough...

[Istvan Albert]

make yourself a smaller reference genome, just the contigs you are interested in