N50 too small

[yaradua]

Hi,

Thank you for developing wtdbg2. I am using wtdbg2 to assemble a genome from Pacbio sequel HIfi reads. The genome size is close to the estimated size from genomescope. I am suspecting that the contigs are too much and another issue is that the N50 is too small. Please advice on how to about it to improve the assembly.

below is the summary of the assembly.

Assembly ShHIFI.srp

contigs (>= 0 bp) 62623

contigs (>= 1000 bp) 62623

contigs (>= 5000 bp) 61594

contigs (>= 10000 bp) 45709

contigs (>= 25000 bp) 16864

contigs (>= 50000 bp) 5611

Total length (>= 0 bp) 1452814764
Total length (>= 1000 bp) 1452814764
Total length (>= 5000 bp) 1447971809
Total length (>= 10000 bp) 1330651245
Total length (>= 25000 bp) 871060639
Total length (>= 50000 bp) 484549799

contigs 62623

Largest contig 2069004
Total length 1452814764
GC (%) 38.79
N50 32012
N90 10740
auN 56529.6
L50 11729
L90 43468

N's per 100 kbp 0.00