How to Use the Command 'mashtree' (with examples)

Mashtree is a powerful bioinformatics tool designed to create a rapid and approximate tree from genome sequences. While it does not produce a phylogeny in the strictest sense, it can process both fastq and fasta files efficiently by utilizing multiple threads. This capability makes mashtree especially useful for researchers who require a quick visualization or general understanding of the relationships between genetic sequences. Below, we’ll explore several use cases offering different levels of speed and accuracy.

Use Case 1: Fastest Method in Mashtree to Create a Tree from Fastq and/or Fasta Files

Code:

mashtree --numcpus 12 *.fastq.gz *.fasta > mashtree.dnd

Motivation: In bioinformatics, speed is often of the essence, particularly when working with large datasets. This use case exploits mashtree’s ability to quickly generate a tree structure by utilizing multiple threads. It’s ideal for scenarios where a researcher needs a quick look at genomic relationships and can compromise a bit on accuracy.

Explanation:

• mashtree: Calls the mashtree command to start processing the files.
• --numcpus 12: Speeds up the computation by using 12 CPU threads simultaneously. This is particularly useful in high-performance computing environments with multiple cores.
• *.fastq.gz *.fasta: Specifies that all files with extensions .fastq.gz and .fasta in the current directory should be included in the analysis. These file extensions represent compressed raw sequencing data and assembled genome sequences, respectively.
• > mashtree.dnd: Redirects the output to a file named mashtree.dnd, typically containing the tree in Newick format – a standard way of representing trees with branch length data.

Example Output: The result is a Newick formatted tree string saved in mashtree.dnd, which could look something like this:

((seq1:0.01,seq2:0.01):0.015,(seq3:0.017,seq4:0.018):0.02);

Use Case 2: Most Accurate Method in Mashtree to Create a Tree from Fastq and/or Fasta Files

Code:

mashtree --mindepth 0 --numcpus 12 *.fastq.gz *.fasta > mashtree.dnd

Motivation: For researchers requiring more precision in tree construction, this use case offers enhanced accuracy by ensuring that all k-mers (subsequences of length k) in the dataset are fully considered. This method is suitable when the quality of the insights significantly impacts the downstream analysis.

Explanation:

• mashtree: Initiates the mashtree tool.
• --mindepth 0: This parameter ensures no minimum depth is set for k-mer coverage, effectively utilizing all data available for a more accurate representation.
• --numcpus 12: Employs 12 CPU threads, enhancing processing speed without compromising accuracy.
• *.fastq.gz *.fasta: Targets all applicable files for analysis.
• > mashtree.dnd: Directs the output and saves it to mashtree.dnd.

Example Output: The output file mashtree.dnd will contain a Newick tree structure that more accurately reflects the relationships described by the input data:

((seq1:0.009,seq2:0.011):0.014,(seq3:0.02,seq4:0.019):0.022);

Use Case 3: Most Accurate Method to Create a Tree with Confidence Values

Code:

mashtree_bootstrap.pl --reps 100 --numcpus 12 *.fastq.gz -- --min-depth 0 > mashtree.bootstrap.dnd

Motivation: For researchers who require not only accuracy but also wish to estimate the confidence of the tree’s branching structure, this methodology provides bootstrapping capabilities. Bootstrapping is a statistical method used to assign confidence estimates to phylogenetic trees, which is crucial for drawing sound conclusions in evolutionary biology.

Explanation:

• mashtree_bootstrap.pl: A Perl script specific to mashtree that allows bootstrapped analysis.
• --reps 100: Sets the number of bootstrap replicates to 100, determining how many times the dataset should be resampled to assess the reliability of the branches.
• --numcpus 12: Employs 12 CPU threads to expedite the computation during the bootstrapping process.
• *.fastq.gz: Specifies the input files for analysis, focusing on fastq.gz files.
• --: A delimiter indicating that the remaining options are directed at the underlying mashtree command.
• --min-depth 0: Ensures all available k-mers are used, providing a comprehensive analysis.
• > mashtree.bootstrap.dnd: Saves the output, including bootstrap values, to mashtree.bootstrap.dnd.

Example Output: The file mashtree.bootstrap.dnd will contain a tree with bootstrap values indicating the reliability of each branch:

((seq1:0.01,seq2:0.01)95:0.015,(seq3:0.017,seq4:0.018)80:0.02);

Conclusion:

Mashtree stands out as a versatile tool that caters to varying needs within genomic studies. Whether you’re a researcher who needs rapid results or one that requires accuracy and confidence, mashtree offers options tailored to meet those needs effectively. Understanding how to balance these parameters can greatly enhance the interpretive value derived from genomic data.