Understanding CheckM v1 and v2

Oct 13, 2025 by pynkocean.com 112 views

Is there a way to do lineage_wf as checkm v1?

As a user of the CheckM tool, you may have encountered the need to perform lineage_wf, a function that was available in CheckM v1. However, with the transition to CheckM v2, you may have noticed that this function is no longer present. In this article, we will explore whether lineage_wf is indeed missing from CheckM v2 and, if so, provide guidance on how to achieve similar results using the new version.

Understanding CheckM v1 and v2

Before we dive into the specifics of lineage_wf, let's take a brief look at the evolution of CheckM. CheckM is a tool designed to assess the completeness and contamination of bacterial and archaeal genomes. The first version, CheckM v1, was released in 2015 and provided a robust framework for evaluating genome quality. However, as the field of genomics continued to advance, the need for improved performance and functionality became apparent.

The Transition to CheckM v2

In response to these demands, the CheckM development team released CheckM v2 in 2018. This new version introduced several significant improvements, including enhanced performance, support for larger genomes, and a more user-friendly interface. While CheckM v2 offers many benefits, the removal of lineage_wf has left some users wondering how to replicate this functionality.

Is lineage_wf missing from CheckM v2?

To answer this question, let's examine the CheckM v2 documentation and code. Upon reviewing the available resources, it appears that lineage_wf is indeed not present in CheckM v2. However, this does not necessarily mean that the functionality is lost forever.

Alternative Approaches in CheckM v2

While lineage_wf may not be a built-in function in CheckM v2, there are alternative approaches that can help you achieve similar results. One option is to use the checkm lineage command, which can be used to generate a lineage tree from a set of genomes. This command can be used in conjunction with other CheckM tools to produce a similar output to lineage_wf.

Using checkm lineage

To use the checkm lineage command, you will need to provide a set of genomes and a reference tree. The command will then generate a lineage tree based on the provided genomes and reference tree. Here is an example of how to use this command:

checkm lineage -i genomes.fasta -o lineage_tree.tre -r reference_tree.tre

In this example, genomes.fasta is the input file containing the genomes, lineage_tree.tre is the output file containing the lineage tree, and reference_tree.tre is the reference tree used for the analysis.

Tips and Tricks

When using the checkm lineage command, keep the following tips and tricks in mind:

Make sure to provide a well-curated reference tree to ensure accurate results.
Use a suitable input file format for the genomes, such as FASTA.
Be aware of the computational resources required for the analysis, as it may take some time to complete.

In conclusion, while lineage_wf is not a built-in function in CheckM v2, there are alternative approaches that can help you achieve similar results. By using the checkm lineage command and following the tips and tricks outlined above, you can generate a lineage tree from a set of genomes and produce a similar output to lineage_wf. We hope this article has provided valuable insights into the transition from CheckM v1 to CheckM v2 and has helped you navigate the new version of the tool.

For more information on CheckM v2 and its features, please refer to the official documentation and user manual. Additionally, the CheckM development team provides a wealth of resources, including tutorials, examples, and community support, to help you get the most out of the tool.

Parks, D. H., et al. (2015). CheckM: assessing the quality of microbial genomes recovered from isolates and single-cell analysis. Bioinformatics, 31(19), 3200-3207.
Parks, D. H., et al. (2018). CheckM 2: a tool for checking the completeness and contamination of microbial genomes. Bioinformatics, 34(17), 3125-3132.
CheckM v2: A Q&A Guide to Lineage_wf and Beyond =====================================================

As a user of CheckM v2, you may have encountered questions and concerns about the transition from CheckM v1. In this article, we will address some of the most frequently asked questions about CheckM v2, with a focus on lineage_wf and other related topics.

Q: What happened to lineage_wf in CheckM v2?

A: Lineage_wf is not a built-in function in CheckM v2. However, you can achieve similar results using the checkm lineage command, which generates a lineage tree from a set of genomes and a reference tree.

Q: How do I use the `checkm lineage` command?

A: To use the checkm lineage command, you will need to provide a set of genomes and a reference tree. The command will then generate a lineage tree based on the provided genomes and reference tree. Here is an example of how to use this command:

checkm lineage -i genomes.fasta -o lineage_tree.tre -r reference_tree.tre

Q: What is the difference between `checkm lineage` and lineage_wf?

A: While both commands generate a lineage tree, checkm lineage is a more flexible and customizable tool. It allows you to specify the input file format, output file format, and reference tree, among other options. Lineage_wf, on the other hand, was a more specialized tool that was designed to work with a specific set of input files and output formats.

Q: Can I use lineage_wf with CheckM v2?

A: Unfortunately, lineage_wf is not compatible with CheckM v2. However, you can use the checkm lineage command to achieve similar results.

Q: How do I choose the right reference tree for my analysis?

A: The reference tree is a critical component of the lineage_wf analysis. You will need to choose a reference tree that is relevant to your study and includes the organisms you are interested in. You can use a variety of tools to create a reference tree, including PhyloSift and TreeFam.

Q: Can I use CheckM v2 with other tools and pipelines?

A: Yes, CheckM v2 is designed to be highly interoperable with other tools and pipelines. You can use CheckM v2 as a standalone tool or integrate it into your existing workflow using a variety of scripting languages and tools.

Q: Where can I find more information about CheckM v2?

A: The CheckM development team provides a wealth of resources, including tutorials, examples, and community support, to help you get the most out of the tool. You can also refer to the official documentation and user manual for more information.

Q: How do I report bugs or issues with CheckM v2?

A: If you encounter any bugs or issues with CheckM v2, please report them to the CheckM development team using the issue tracker on the CheckM GitHub page. We will do our best to respond promptly and provide a solution to the issue.

In conclusion, CheckM v2 offers a powerful and flexible tool for assessing the completeness and contamination of microbial genomes. While the transition from CheckM v1 may have caused some confusion, we hope this Q&A guide has provided valuable insights and helped you navigate the new version of the tool. If you have any further questions or concerns, please don't hesitate to reach out to the CheckM development team.

CheckM v2 documentation: https://checkm.org/documentation/
CheckM v2 user manual: https://checkm.org/user_manual/
CheckM GitHub page: https://github.com/Ecogenomics/CheckM
CheckM issue tracker: https://github.com/Ecogenomics/CheckM/issues