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?