Question: WGS analysis suggestions
0
gravatar for madhubhaniesenadheera
3.7 years ago by
Sri Lanka
madhubhaniesenadheera0 wrote:

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?

de novo wgs ion torrent • 1.1k views
ADD COMMENTlink modified 3.6 years ago by Biostar ♦♦ 20 • written 3.7 years ago by madhubhaniesenadheera0
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