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adding microGalaxy tag to the new training #4573

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Dec 6, 2023
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adding microGalaxy tag to the new training #4573

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1 change: 1 addition & 0 deletions topics/metagenomics/tutorials/metagenomics-binning/tutorial.md
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tags:
- binning
- metagenomics
- microgalaxy
---

Metagenomics is the study of genetic material recovered directly from environmental samples, such as soil, water, or gut contents, without the need for isolation or cultivation of individual organisms. Metagenomics binning is a process used to classify DNA sequences obtained from metagenomic sequencing into discrete groups, or bins, based on their similarity to each other.
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In this tutorial we will learn how to use **MetaBAT 2** tool through Galaxy. **MetaBAT** stands for "Metagenome Binning based on Abundance and Tetranucleotide frequency". It is:

> *Grouping large fragments assembled from shotgun metagenomic sequences to deconvolute complex microbial communities, or metagenome binning, enables the study of individual organisms and their interactions. Here we developed automated metagenome binning software, called MetaBAT, which integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency. On synthetic datasets MetaBAT on average achieves 98percent precision and 90% recall at the strain level with 281 near complete unique genomes. Applying MetaBAT to a human gut microbiome data set we recovered 176 genome bins with 92% precision and 80% recall. Further analyses suggest MetaBAT is able to recover genome fragments missed in reference genomes up to 19%, while 53 genome bins are novel. In summary, we believe MetaBAT is a powerful tool to facilitate comprehensive understanding of complex microbial communities ({%cite Kang2019%}).*

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topics/metagenomics/tutorials/metagenomics-binning/tutorial.md:168: Potential broken box. A None was opened on 167, but not closed on line 168

We will use the uploaded assembled fasta files as input to the algorithm (For simplicity reasons all other parameters will be preserved with their default values).

> <hands-on-title>Individual binning of short-reads with MetaBAT 2</hands-on-title>
> 1. {% tool [MetaBAT 2](toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy0) %} with parameters:
> - *"Fasta file containing contigs"*: `assembly fasta files`

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topics/metagenomics/tutorials/metagenomics-binning/tutorial.md:174: Potential broken box. A hands_on was opened on 171, but not closed on line 174
<!-- > - In *Advanced options*
> - *"Percentage of good contigs considered for binning decided by connection among contigs"*: `default 95`
> - *"Minimum score of an edge for binning"*: `default 60`
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> - *"Minimum size of a bin as the output"*: `default 200000`
> - *"Output only sequence labels as a list in a column without sequences?"*: `default "No"`
> - *"Save cluster memberships as a matrix format?"*: `"Yes"` -->
>

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topics/metagenomics/tutorials/metagenomics-binning/tutorial.md:188: A None was opened, but closed with hands_on on line 188
{: .hands_on}

The output files generated by MetaBAT 2 include (some of the files below are optional and not produced unless it is required by the user):
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> <hands-on-title>Assessing the completeness and contamination of genome bins using lineage-specific marker sets with `CheckM lineage_wf`</hands-on-title>
> 1. {% tool [CheckM lineage_wf](toolshed.g2.bx.psu.edu/repos/iuc/checkm_lineage_wf/checkm_lineage_wf/1.2.0+galaxy0) %} with parameters:
> - *"Bins"*: `Folder containing the produced bins`

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<!-- > - In *Advanced options*
> - *"Percentage of good contigs considered for binning decided by connection among contigs"*: `default 95`
> - *"Minimum score of an edge for binning"*: `default 60`
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> - *"Minimum size of a bin as the output"*: `default 200000`
> - *"Output only sequence labels as a list in a column without sequences?"*: `default "No"`
> - *"Save cluster memberships as a matrix format?"*: `"Yes"` -->
>

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topics/metagenomics/tutorials/metagenomics-binning/tutorial.md:317: A None was opened, but closed with hands_on on line 317
{: .hands_on}

> <comment-title></comment-title>
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