Supply Chain Security
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Unpopular package
QualityThis package is not very popular.
Found 1 instance in 1 package
Potential vulnerability
Supply chain riskInitial human review suggests the presence of a vulnerability in this package. It is pending further analysis and confirmation.
Found 1 instance in 1 package
Shell access
Supply chain riskThis module accesses the system shell. Accessing the system shell increases the risk of executing arbitrary code.
Found 1 instance in 1 package
Uses eval
Supply chain riskPackage uses dynamic code execution (e.g., eval()), which is a dangerous practice. This can prevent the code from running in certain environments and increases the risk that the code may contain exploits or malicious behavior.
Found 1 instance in 1 package
Welcome.
SingleM is a tool for profiling shotgun metagenomes. It has a particular strength in detecting microbial lineages which are not in reference databases. The method it uses also makes it suitable for some related tasks, such as assessing eukaryotic contamination, finding bias in genome recovery, and lineage-targeted MAG recovery.
Documentation can be found at https://wwood.github.io/singlem/
Community profiles for many publicly available metagenomes can be found at the Sandpiper website.
The overall citation for SingleM/Sandpiper:
Woodcroft, Ben J., Samuel TN Aroney, Rossen Zhao, Mitchell Cunningham, Joshua AM Mitchell, Linda Blackall, and Gene W. Tyson. SingleM and Sandpiper: Robust microbial taxonomic profiles from metagenomic data. bioRxiv (2024): 2024-01. https://doi.org/10.1101/2024.01.30.578060
The microbial_fraction (SMF) mode of SingleM:
Eisenhofer, Raphael, Antton Alberdi, and Ben J. Woodcroft. Large-scale estimation of bacterial and archaeal DNA prevalence in metagenomes reveals biome-specific patterns. bioRxiv (2024): 2024-05. https://doi.org/10.1101/2024.05.16.594470
FAQs
Novelty-inclusive microbial community profiling of shotgun metagenomes
We found that singlem demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 2 open source maintainers collaborating on the project.
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