Currently we are doing a Nematode WGS research. We used ion xpress plus library kit (Single end). We performed 400bp sequencing in ION PGM. We performed 4 sequencing runs.
1st run: 2,573,647 reads (Mean length -129bp) Quality trimmed at the length 100bp and quality 16 threshold
2nd run: 1,732,693 reads (Mean length -193bp) Quality trimmed at the length 100bp and quality 16 threshold
3rd run: 4,757,296 reads (Mean length -229bp) Quality trimmed at the length 250bp and quality 16 threshold
4th run: 4,628,974 (Mean length -155bp) Quality trimmed at the length 300bp and quality 16 threshold
We performed mira de novo for each run and output was mapped with a reference genome. Our assembly reference sequence is having length about 80mb to 100mb.
From the 3rd run output,
Number of contigs: 31750
Total consensus: 70998479
Largest contig: 37395
N50 contig size: 3445
N90 contig size: 944
N95 contig size: 720
What would be the quality parameters for WGS analysis in ION PGM sequencing?
Any suggestions to improve the analysis?
What would be more effective tools to analyze this data?
Assessing The Quality Of De Novo Assembled Data
How To Assess The Quality Of An Assembly? (Is There No Magic Formula?)