Denoise App Free Download
Shara Mchale
I am test running dada2 denoise-paired for a subsample of 16 samples (4,5 Gb) bacterial 16s sequences on Miseq ( I have 350 samples in total). I imported the demultiplexed files like this, the qza file is 981M:
And I am running dada2 denoise-paired for more than 12 hours, is this normal run time, it seems longer than reported from others. Could it be a problem with how I imported the files to qiime"?? What can I expect the running time for the full sample set of 350 samples? I did not get any error yet, however I dont see any output from verbose as I had to relaunch the terminal window. ( I am running qiime through remote access).
I am trying to run Dada2 denoise-paired for more than 12 hours using several theads with a subsample of 16 samples. My real set consists of 350 samples. currently using 425 % CPU I imported the demultiplexed files like this:
Well I hope I am not just adding noise to this conversation . But I opened an image shot from a Canon G16, which is a quality compact camera, shot at 1600 ISO. I applied no processing to the image and have cropped a section of the image for comparison. The section on the left has no noise reduction, the centre one has denoise (profile) at default settings, and the one on the right has RAW denoise default settings. For my two cents worth, I find the denoise (profile) has become my default denoise method. With really troublesome images I may also recruit various other modules including the Contrast equalizer module and maybe even Raw denoise. I feel the denoise (profiled) module works so much better since DT V4.0 for my cameras.
image1461446 460 KB
But I opened an image shot from a Canon G16, which is a quality compact camera, shot at 1600 ISO. I applied no processing to the image and have cropped a section of the image for comparison. The section on the left has no noise reduction, the centre one has denoise (profile) at default settings, and the one on the right has RAW denoise default settings. For my two cents worth, I find the denoise (profile) has become my default denoise method. With really troublesome images I may also recruit various other modules including the Contrast equalizer module and maybe even Raw denoise. I feel the denoise (profiled) module works so much better since DT V4.0 for my cameras.
As you say it is to taste, as is sharpening, and in some areas of photography, people can get very picky. I am happy that I can reduce it enough for my needs. I was just observing that, if I do it with Denoise (profiled), I get more artifacts, than raw denoise, but as someone said, maybe I am losing more detail with raw denoise. Anyway, no matter the method, I take the advice not to go too hard.
As kofa says it would be good to see an example. Then we are all talking about the same thing when we make comments. With the xmp files we can all see what settings and other modules are being used so we understand the full picture. For example it would be good to see what you call artifacts.with profiled denoise also when I have played with raw denoise in the past it has been my experience that just turning it on obliterate the detail so I am sure you tweak it and it would interesting to see your process
The reason I use the contrast equalizer module to tackle luma noise is that it has minimal loss of detail because you can control the size of the wavelets being tackled. The denoise profiled tends to handle chroma noise beautifully and reduces luma noise. With contrast equalizer I only worry about the luma noise.
The sample image attached is left panel no noise reduction, centre panel denoise profiled, and right panel denoise profile and Contrast Equalizer used as shown in separate image. All of these panels have demosiacing sharpening from the new diffuse or sharpen module. Considering the high ISO and small image sensor I am more than happy with this result. Only a small section of the whole image is shown here.
The truth is that I am so happy with the default settings on denoise profile with my camera images that I have not invested time yet into manually tweaking it. With really noisy images I increase the strength of the default values. When I have a suitable image that justifies the time I may explore what you are suggesting.