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?