数据与复现生物信息与基因组学FreedomIntelligence/OpenClaw-Medical-Skills数据与复现

bio-metagenomics-abundance

维护者 FreedomIntelligence · 最近更新 2026年4月1日

Species abundance estimation using Bracken with Kraken2 output. Redistributes reads from higher taxonomic levels to species for more accurate estimates. Use when accurate species-level abundances are needed from Kraken2 classification output.

OpenClawNanoClaw分析处理复现实验bio-metagenomics-abundance🧬 bioinformatics (gptomics bio-* suite)bioinformatics — metagenomics & microbiomespecies

原始来源

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-metagenomics-abundance

维护者: FreedomIntelligence
许可: MIT
最近更新: 2026年4月1日

技能摘要

来自 SKILL.md 的关键信息

2 min

核心说明

CLI：bracken -d db -i kraken2.report -o bracken.output -r 150 -l S。
Get species-level abundances ，面向 my Kraken2 results" → Redistribute reads assigned to higher taxonomic levels down to species ，使用 Bracken's Bayesian re-estimation ，用于 more accurate abundance profiles. CLI：bracken -d db -i kraken2.report -o bracken.output -r 150 -l S。
bracken -d /path/to/kraken2_db \ -i kraken_report.txt \ -o bracken_output.txt \ -r 150 \ # Read length (100，150，200，250，300) -l S # Taxonomic level。

原始文档

SKILL.md 摘录

Step 1: Classify with Kraken2

kraken2 --db /path/to/kraken2_db
--threads 8
--paired
--report sample_kraken_report.txt
reads_R1.fastq.gz reads_R2.fastq.gz

Step 2: Estimate abundances with Bracken

bracken -d /path/to/kraken2_db
-i sample_kraken_report.txt
-o sample_bracken_species.txt
-w sample_bracken_report.txt
-r 150
-l S


## Species level (default)

bracken -d db -i report.txt -o species.txt -r 150 -l S

适用场景

适合在accurate species-level abundances are needed ，面向 Kraken2 分类 output时使用。

不适用场景

Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。

上游相关技能

kraken-classification - Generate Kraken2 report
metaphlan-profiling - Alternative profiling method
metagenome-visualization - Visualize abundances

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