Entering edit mode
3.5 years ago
a4appy23
▴
50
This is a basic question. I have a genome A . when I ran quast the on the genome A that is downloaded from NCBI it had N50 of 20,634,945. when i used soap denovo 2 to reconstruct the genome A with aired end reads of genome A .The contig level assembly had N50 2669 and the scaffolds had a N50 of 253411. Now im wondering why is the N50 reconstructed by denovo assembler is low than the N50 of original genome. did i do some thing wrong or this is how the assembler reconstructs.
Are you assembly the same dataset? Any kmer-based assembler will need to tweak the kmer value (or use multiple sets) to get a good assembly.
Im trying to reconstruct a contig level assembly using genome A reads. i tried with k31 and k51 and chose k51 because it gave higher contigs compared to k31. but in this scenario 2641 is very low
How is this very good ? Are you mixing up reads and contigs ? Why were you doing Quast before assembly ? Please make your question more understandable, thanks.
Getting 2600 contigs from a pure Illumina PE assembly seems quite reasonable to me. If it is a small genome you can try Spades as well.