contamination 开源项目推荐（86 个）

DRL /blobtools

Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets

benjjneb /decontam

Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data

microsoft /MMLU-CF

A Contamination-free Multi-task Language Understanding Benchmark [Official, ACL 2025]

Griffan /VerifyBamID

verifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.

khyox /recentrifuge

Recentrifuge: robust comparative analysis and contamination removal for metagenomics

StevenWingett /FastQ-Screen

Detecting contamination in NGS data and multi-species analysis

kMegapnbedt /Bench-B

Benchmark contamination forensics: exact n-gram containment scanning in pure Python plus a C++17 MinHash engine (bloomdex) for corpus-scale leakage checks.

hitz-zentroa /lm-contamination

The LM Contamination Index is a manually created database of contamination evidences for LMs.

CMU-SAFARI /RawHash

RawHash 能够实时准确高效地将原始纳米孔信号映射到不同大小的参考基因组（例如从病毒到人类基因组），无需碱基调用。由 Firtina 等人描述（发表于 https://academic.oup.com/bioinformatics/article/39/Supplement_1/i297/7210440 年）。

LaVi-Lab /CLEVA

[EMNLP 2023 Demo] "CLEVA: Chinese Language Models EVAluation Platform"

mbhall88 /nohuman

Remove human reads from a sequencing run

Plant-Food-Research-Open /assemblyqc

A Nextflow pipeline for evaluating assembly quality

HaoGroup-ProtContLib /Protein-Contaminant-Libraries-for-DDA-and-DIA-Proteomics

该项目由马里兰大学帕克分校化学与生物化学系的 Hao 实验室创建。该项目旨在提供可普遍应用于 DDA 和 DIA 蛋白质组学的污染蛋白 FASTA 和谱库，并向蛋白质组学社区免费开放。

seppinho /mutserve

mtDNA Variant Caller

pirovc /grimer

GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and metadata with focus on contamination detection.

Arkadiy-Garber /SprayNPray

Rapid and simple taxonomic profiling of genome and metagenome contigs

mpieva /mapping-iterative-assembler

Consensus calling (or "reference assisted assembly"), chiefly of ancient mitochondria

rabbittsui /EvalLeak

Detect contamination between training and evaluation splits - exact duplicates, near duplicates, and containment across split manifests.

castro-gzlz /TESS-cont

Flux contamination analysis (TESS)

htafer /remoVecSec

Module and script to remove contamination in assembled genomes before submission to ncbi