Tutorials on How-to-Do NGS Data Analysis in the AWS Cloud with a Graphical User Interface (GUI)

At this page you can find an index of all available tutorials from DocMind Analytics. They will teach you how to use our free DocMind Analyst software for Next-Generation-Sequencing (NGS) data analysis on your AWS cloud computer. The DocMind Analyst will provide a graphical user interface (GUI) for popular bioinformatics tools and will enable you to set up analytical pipelines without any knowledge of command line or programming languages. After the setup, you can conduct your big data analysis on high-end computers at any time and from anywhere in the world. At a first step, you just need to watch the introduction to AWS cloud computing tutorial. It will provide you with the basics of cloud computing and show you what software you need to make it run and to transfer files to your cloud computer. It is very easy and you will be able to set up your cloud computer in a couple of minutes. When you are familiar with these basics, you can watch the second video tutorial on how to start a cloud computer that contains the free DocMind Analyst software and on how you can you can use the software. Afterwards, focus on the analysis of your interest and watch the particular tutorial videos. They won’t just show you how to use our DocMind Analyst software but also how popular bioinformatics tools are set up and which parameters are appropriate for your analysis. Enjoy watching!

Introduction to AWS cloud computing on an Ubuntu 16.04 system with a graphical user interface. 

Introduction to the DocMind Analyst software tool. 

1. Basic Analysis and Processing of Short Sequence Read Data

All at once – The Short Read Assembly Pipeline

Learn how to perform all steps of an whole genome sequencing assembly in one analysis.  

Trim your Sequence Reads and perform Quality Control

Learn how to clean your reads with Trimmomatic and check quality with FastQC.  

Genome Assembly Module using the SPAdes Assembler

Learn how to assemble bacterial genomes from short sequence reads using SPAdes.  

Genome Assembly Module using the A5 MiSeq Assembler

Learn how to assemble bacterial genomes from short sequence reads using A5.  

Genome Assembly Module using the novel Skesa Assembler

Learn how to assemble bacterial genomes from short sequence reads using Skesa.  

Increase Assembly Quality by Postprocessing with Pilon

Learn how to perform a postprocessing and how to improve assembly quality.  

Use the DocMind Analyst Statistics for Assembly Quality Control 

Learn how to perform and interpret statistics of your WGS assembly    

2. Molecular Phylogeny of Whole Genome Assembly Data

Core Genome Phylogeny Pipeline at one Glance

Learn how to construct a core genome, call SNPs/Indels on reference genomes and perform a phylogenetic reconstruction.  

Core Genome Construction using Spine with a GUI

Learn how to construct a core genome and how to handle different parameter during construction. Use the DocMind Analyst GUI. 

Perform a professional SNP/Indel Calling and Filtering

Learn how to call SNPs/Indels on reference genomes using samtools/bcftools. Filter SNPs according to your research objectives.  

Multiple Alignment Generation using the DocMind Analyst GUI

Learn how to generate a multiple alignment from VCF file output from samtools.  Use the alignment for phylogenetic analyses. 

Phylogenetic Reconstruction using Gubbins

Learn how to perform a maximum likelihood phylogeny using Gubbins and take genomic recombination into account.   

Phylogenetic Reconstruction using IQTree

Learn how to use one of the fastest available phylogeny tool. A perfect fit for genomic alignments with thousands of WGS sequences. 

Phylogenetic Reconstruction using FastTree

Learn how to set up a phylogentic analysis with FastTree and handle it easily with the graphical user interface of the DocMind Analyst.  

Phylogenetic Reconstruction using RAxML

Learn how to make use of the most popular phylogenetic reconstruction tool with the DocMind Analyst software.   

Visualize your Phylogenetic Tree with FigTree

Learn how to convert your tree file into a professional figure with various options for displaying youtrtree.  

Utilize SplitsTree for Alignment Analysis 

Learn how to use the populat SplitsTree in order to display the underlying structure of your WGS alignment.  

Visualize your Genomic Mapping Results with the Broad Institute’s IGV 

Learn how to see the results of your genomic mapping (BAM files) using the Integrative Genomic Viewer (IGV).  

3. 16S rRNA based Microbiome Analysis

Taxonomic Microbiome Reconstruction Pipeline using 16S rRNA sequence data

Learn how to reconstruct the taxonomic microbiome composition from 16S rRNA sequencing.

Chimera Removal using the Mothur Software Suite

Learn how to clean your 16S rRNA sequence reads form chimera contamination.

16S rRNA Taxonomic Classification with RDP

Learn how to run a taxonomic classification of 16S rRNA  sequence reads using RDP.

Hierarchical clustering of 16S rRNA taxonomic data 

Learn how to cluster your taxonomic data sets  in relation to samples and taxa.

4. General Analysis Tools

Rename Thousand Files at Once 

Learn how to rename many files and make them fit for analytical pipelines.

5. Troubleshooting

“Q” in Monitor after Job Start 

Learn how to deal with the “Q” in the Monitor Panel after you have started a job.

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