Tool: DocMind Analyst - A New NGS Data Analysis Software Suite With A Graphical User Interface Specifically Designed For Researchers Without Bioinformatics Background
2
gravatar for DMA
19 days ago by
DMA20
Tuebingen, Germany, DocMind Analytics
DMA20 wrote:

Hi,

We would like to present DocMind Analyst, a collection of popular bioinformatics tools that can be easily handled with a graphical user interface without any programming or bioinformatics skills. It is specifically designed for researchers in microbiology and infectious diseases who want to analyze their NGS data but have no computer science background. You can run entire analytical pipelines and select the tools you would like to use. There are video and text tutorials for each module of the pipelines, and every parameter as well as computational requirements are explained in detail. It is thus mostly intended for beginners although experts might also find some convenient analysis options. DocMind Analyst allows you to:

  • Trim sequence reads and remove adapters (Trimmomatic)
  • Analyze the quality of sequence reads (FastQC)
  • Assemble genomes (SPAdes, A5, Skesa)
  • Assembly postprocessing (Pilon)
  • Assembly statistics (including visualization) and MLST typing
  • Core genome generation (Spine)
  • SNP and Indel calling (samtools)
  • Phylogenetic analysis (Gubbins, FastTree, IQTree, RAxML), including outbreak investigation
  • Phylogenetic tree visualization and minimum spanning tree generation (FigTree, SplitsTree)
  • 16S rRNA microbiome analysis and classification (RDP)
  • Chimeric read removal with Mothur
  • Microbiome heatmap visualization

Output files include data visualization, specific output (like Fasta) and common CSV files which can easily be imported in Excel for downstream analysis and graphical presentations. The software runs in the Amazon Web Services cloud and is free. It scales according to your requirements. You can run a few samples but also thousands by adapting the computational power you need. You can start the software from Windows and Mac OS.

DocMind Analyst will be further developed and will implement more functions. If you are interested you can participate in a survey and let us know which function would be most important for you.

DocMind Analyst Graphical User Interface - 16S rRNA Analysis Panel

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Microbiome Pattern Of Three Samples Displayed In A Heatmap

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Minimum Spanning Tree

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ADD COMMENTlink written 19 days ago by DMA20

Software is free but you pay for your own AWS costs as noted by @DMA here : C: genome assembly software

ADD REPLYlink modified 19 days ago • written 19 days ago by genomax58k

That's correct. You need to pay for cloud infrastructure. This can be done on an on-demand base. Good thing is that you don't need to invest in a heavy computer and you just pay for what you use. This can be a great cost-saving strategy when your group needs to analyze a bunch of data from time to time and not everyday (like in most research settings). In any case, you can try the software without paying since AWS offers a free t2.micro instance within the first year after registration. It's good to check out the system though I can't recommend that you run a lot of analyses. This could take forever...

ADD REPLYlink written 19 days ago by DMA20
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