Mapler

Mapler evaluates and compares the quality of metagenome assemblies from taxonomically complex microbial communities sequenced with HiFi reads.

Key Features:

• Assembly quality assessment: Incorporates several state-of-the-art metrics for evaluating HiFi long read metagenome assemblies.
• Uncaptured diversity metrics: Includes novel metrics that assess the diversity remaining unassembled after the assembly process.
• Assembly strategy comparison: Facilitates direct comparison of different assembly strategies to identify methodological bottlenecks in genome reconstruction.

Scientific Applications:

• Complex environmental metagenomics: Evaluates assembly quality in samples containing hundreds to thousands of microbial populations.
• HiFi read metagenome assembly optimization: Identifies methodological bottlenecks that hinder genome reconstruction from PacBio HiFi sequencing data.

Methodology:

Mapler is implemented as a Snakemake pipeline in Python and Bash.