Biomedical Data Analysis Platform

Lineage Placement: Assigns each bin to a taxonomic lineage based on marker gene content.
Marker Analysis: Identifies presence/copy number of lineage-specific single-copy markers.
Quality Estimation: Calculates completeness (% markers found) and contamination (% markers with >1 copy).
Output: Generates summary table, plots, and per-bin statistics.

Data

Output files of Binning algorithm

Results

quality_report.tsv

Versions

v1.0: Process construction, complete the basic process of data quality assessment

Usage

1. Select the application 'Binning evaluate'
2. Click on the 'Analysis' button
3. Click on the 'checkm2'
4. Click on the 'Add Option' to add fileName from self upload, and then fill in the request parameters

Core Parameters

Parameter	Description
`lineage_wf`	Standard workflow for MAGs. Use `taxonomy_wf` for isolate genomes.
`-t`	Threads.
`-x`	Bin file extension (`fa`, `fna`, `fasta`).
`--tab_table`	Output tab-separated summary (essential for downstream filtering).
`-r`	Reduced tree mode (faster, slightly less accurate).
`--pplacer_threads`	Threads for pplacer step (often bottleneck).

Example

checkm lineage_wf -t 16 -x fa --tab_table bins/ checkm_results