Open DorothyTamYiLing opened 1 year ago
Hello, Dorothy!
I share the same question and concern. I've observed that as the contig size decreases, the depth increases. I'm uncertain whether an assembly with a depth of 1.00x is considered a satisfactory outcome. I'm hopeful that someone with knowledge in this area can provide an answer, as it would be greatly appreciated.
Here's the information on my contigs for hybrid assembly:
>1 length=2520275 depth=1.00x circular=true
>2 length=138051 depth=1.24x circular=true
>3 length=15903 depth=1.55x circular=true
>4 length=5174 depth=7.63x circular=true
>5 length=3191 depth=10.60x circular=true
Thank you!
Maybe the short ones are caused by multiple copies of plasmids in the bacteria, since the five short contigs are all circular.
Hi Ryan,
Thanks for writing Unicycler, it is a very useful tool.
I ran a hybrid assembly using conservative mode (same result for normal mode) and I obtained 3 contigs, as follows:
I blasted the two small contigs with the big one and there were present, although contig 3 showed a few mismatches:
qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore 2 1 100.00 1905 0 0 1 1905 1993753 1991849 0.0 3518 3 1 99.31 1590 11 0 6 1595 2457094. 2455505 0.0 2876
I would like to know if contig 1 is a good quality assembly for use, as well as why the two small contigs show less than 1 fold of coverage?
Thanks, Dorothy