Merge pull request #96 from jolespin/devel

v2.0.0

FAQ.md

@@ -4,7 +4,7 @@
 ______________________
 #### *VEBA* has so many modules and capabilities, how can I get a feel for how to use it for my dataset(s)?
 
-Check out the [walkthroughs](https://github.com/jolespin/veba/tree/main/walkthroughs) where there are step-by-step workflows for different types of data.
+Check out the [walkthroughs](https://github.com/jolespin/veba/tree/main/walkthroughs) where there are step-by-step workflows for different types of data.  For a visual walkthrough of the modules, watch the [Getting started with VEBA](https://www.youtube.com/watch?v=pqrIffWNuug) YouTube video. There are several video tutorials on our [YouTube Channel @VEBA-Multiomics](https://www.youtube.com/@VEBA-Multiomics) covering topics such as how to get started, how to install/configure databases, custom installations/databases, Docker usage on local machines, and the end-to-end walkthrough in real-ish time.
 
 <p align="right"><a href="#faq-top">^__^</a></p>
 
@@ -28,7 +28,7 @@ Since this is more advanced usage, you'll have to go through and comment out the
 ______________________
 
 
-### How can I install just a single module and a subset of the database required for that module?
+#### How can I install just a single module and a subset of the database required for that module?
 
 This can be done easily with a custom installation.  For example, let's say you want to only use the `annotate.py` module.  You would go to the [module table](https://github.com/jolespin/veba/blob/main/bin/README.md) to see that `annotate.py` module uses the `VEBA-annotate_env` and the `Annotate` database.  Then you would install the custom build as follows:
 
@@ -644,7 +644,7 @@ Are there any large contigs? What's the N50?
 
 ______________________
 
-### How can I use Docker or Singularity to run VEBA?
+#### How can I use Docker or Singularity to run VEBA?
 
 Check out the [*VEBA* walkthroughs for Docker, Singularity, and AWS](https://github.com/jolespin/veba/tree/main/walkthroughs#containerization-and-aws).
 

README.md

@@ -15,7 +15,7 @@
 [issues-shield]: https://img.shields.io/github/issues/jolespin/veba.svg?style=for-the-badge
 [issues-url]: https://github.com/jolespin/veba/issues
 
-[![Schematic](images/graphical-abstract.png)](images/Schematic.pdf)
+[![Schematic](images/graphical-abstract.png)](images/graphical-abstract.pdf)
 
 ### What is VEBA? 
 The *Viral Eukaryotic Bacterial Archaeal* (VEBA) is an open-source software suite developed with all domains of microorganisms as the primary objective (not post hoc adjustments) including prokaryotic, eukaryotic, and viral organisms.  VEBA is an end-to-end metagenomics and bioprospecting software suite that can directly recover and analyze eukaryotic and viral genomes in addition to prokaryotic genomes with native support for candidate phyla radiation (CPR). VEBA implements a novel iterative binning procedure and an optional hybrid sample-specific/multi-sample framework that recovers more genomes than non-iterative methods.  To optimize the microeukaryotic gene calling and taxonomic classifications, VEBA includes a consensus microeukaryotic database containing protists and fungi compiled from several existing databases. VEBA also provides a unique clustering-based dereplication strategy allowing for sample-specific genomes and proteins to be directly compared across non-overlapping biological samples. VEBA also automates biosynthetic gene cluster identification and novelty scores for bioprospecting.

images/Schematic/Schematic_v1.1.x.gslides

@@ -1 +1 @@
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images/Schematic/Schematic_v1.2.0.gslides

@@ -1 +1 @@
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images/Schematic/Schematic_v2.0.0.gslides

@@ -1 +1 @@
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