Binning tutorial update

[paulzierep]

This will be a major update adding 3 binners, mapping and bin refinement,
I probably also need to update the test data, keeping it smaller.

Takes over this one: #6409
Thanks a lot for the start @vinisalazar.

[paulzierep]

@bebatut this is ready for review ! One thing to add is the note to look into the MAG full tutorial for some stuff, but I will add this once yours is ready !

[bebatut]

Thanks a lot @paulzierep and @vinisalazar for this update.
I added suggestions, mostly text clarification/correction and sometimes some reorganization between text and hands-on

[bebatut]

Suggested change

	## Binning challanges
	## Binning challenges

[bebatut]

Suggested change

	# Mock binning dataset for this training
	## Mock binning dataset for this training

[bebatut]

Suggested change

	Read mapping and binning real metagenommic datasets is a computational demanding task and time consuming. To demonstrate the basics of binning in this tutorial we generated a small mock dataset, that is just large enough to produce bins for all binners in this tutorial. The same binners can be applied for any real life datasets, but as said, plan in some time, up to weeks in some cases.
	Read mapping and binning real metagenomic datasets is a computationally demanding and time-consuming task. To demonstrate the basics of binning in this tutorial, we generated a small mock dataset that is just large enough to produce bins for all binners in this tutorial. The same binners can be applied for any real-life datasets, but as said, plan in some time, up to weeks in some cases.

[bebatut]

Suggested change

	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.
	Metagenomics is the study of genetic material recovered directly from environmental samples, such as soil, water, or gut contents, without the need for isolating or cultivating 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.

[bebatut]

Suggested change

The goal of metagenomics binning is to assign the DNA sequences to the organisms or taxonomic groups that they originate from, allowing for a better understanding of the diversity and functions of the microbial communities present in the sample. This is typically achieved through computational methods that include sequence similarity, composition, and other features to group the sequences into bins.

The goal of metagenomics binning is to assign DNA sequences to the organisms or taxonomic groups from which they originate, allowing for a better understanding of the diversity and functions of the microbial communities present in the sample. This is typically achieved through computational methods that include sequence similarity, composition, and other features to group the sequences into bins.

[bebatut]

Suggested change

## Bin contigs using MaxBin2

[bebatut]

Suggested change

	In this tutorial version we will learn how to use MaxBin2 {%cite maxbin2015%} through Galaxy. MaxBin2 is an automated metagenomic binning tool that uses an Expectation-Maximization algorithm to group contigs into genome bins based on abundance, tetranucleotide frequency, and single-copy marker genes.
	**MaxBin2** ({% cite maxbin2015 %}) is an automated metagenomic binning tool that uses an Expectation-Maximization algorithm to group contigs into genome bins based on abundance, tetranucleotide frequency, and single-copy marker genes.

[bebatut]

Suggested change

The first step when using tools like MetaBAT or MaxBin2 is to compute contig depths from the raw alignment data. Both tools require per-contig depth tables as input, as their binning algorithms rely on summarized coverage statistics at the contig level. However, standard BAM files store read-level alignment information, which must first be processed to generate the necessary contig-level coverage data. This preprocessing step ensures compatibility with the input requirements of these binning tools.

[bebatut]

Suggested change

	> > <comment-title> Why not use bam directly </comment-title>
	> >
	> > MetaBAT and MaxBin2 only accept per-contig depth tables because that is the specific input format their binning algorithm requires.
	> > BAM files contain read-level alignment data.
	> > These binners need summarized, contig-level coverage statistics.
	> {: .comment}

[bebatut]

Suggested change

	We can now launch the proper binning with MaxBin2

[bebatut]

Thanks a lot @paulzierep and @vinisalazar for this update.
I added suggestions, mostly text clarification/correction and sometimes some reorganization between text and hands-on