Runs nf-core/bactmap to map bacterial WGS reads and generate phylogenies.
npx skills add https://github.com/danilomonge/nf-claw --skill bactmap
Please help me install this Agent Skill. Skill: bactmap Source: https://github.com/danilomonge/nf-claw/tree/main/pipelines/bactmap Command: npx skills add https://github.com/danilomonge/nf-claw --skill bactmap
This Skill removes the guesswork from running the nf-core/bactmap pipeline so you can map bacterial whole-genome sequencing reads against a reference, produce reliable variant and pseudogenome outputs, and optionally generate a phylogeny from the resulting alignments.
Ask me to run bactmap for your bacterial sequencing data by providing the reference genome, input sample information, output directory, and desired Nextflow profile.
High-intent search queries and answers about installing and using this skill.
To map bacterial WGS reads against a reference genome, you need a parameter-driven workflow that processes short reads, calls variants, and builds pseudogenomes. The bactmap pipeline handles this by validating runtime parameters and executing Nextflow for reproducible read mapping.
Yes, you can build a phylogeny from bacterial genome alignments using Nextflow. The pipeline optionally infers phylogenetic trees from pseudogenome alignments generated during the mapping process, with optional subsampling controls for larger datasets.
To run nf-core/bactmap for bacterial variant calling, you need to provide a reference genome path, input sample information, an output directory, and a desired Nextflow profile. The pipeline validates these required parameters before execution.
A pseudogenome workflow generates filtered VCFs by mapping short reads to a reference, identifying variants, and applying filtering criteria. The bactmap pipeline produces these filtered VCFs and pseudogenomes as outputs for downstream comparative genomics analysis.
The best way to ensure reproducible bacterial genome mapping is through version pinning and provenance-aware execution. The bactmap pipeline handles version tracking and provenance recording during Nextflow execution to guarantee reproducible phylogeny generation.
Yes, the bactmap pipeline supports subsampling for large bacterial WGS datasets. It includes optional tree-building and subsampling controls that allow you to manage computational load when inferring phylogenies from extensive genome alignments.
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