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

• UpdatedAug 21, 2024
• Python

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

• UpdatedMar 22, 2023
• R

A Contamination-free Multi-task Language Understanding Benchmark

• UpdatedJan 9, 2025

VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.

• UpdatedMay 21, 2024
• mupad

Recentrifuge: robust comparative analysis and contamination removal for metagenomics

• UpdatedMar 14, 2025
• Python

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

• UpdatedApr 11, 2024
• Python

Detecting contamination in NGS data and multi-species analysis

• UpdatedNov 4, 2024
• HTML

RawHash can accurately and efficiently map raw nanopore signals to reference genomes of varying sizes (e.g., from viral to a human genomes) in real-time without basecalling. Described by Firtina et al. (published athttps://academic.oup.com/bioinformatics/article/39/Supplement_1/i297/7210440).

• UpdatedDec 9, 2024
• C

Remove human reads from a sequencing run

• UpdatedOct 1, 2024
• Rust

mtDNA Variant Caller

• UpdatedDec 23, 2024
• Java

A Nextflow pipeline for evaluating assembly quality

• UpdatedMar 13, 2025
• Nextflow

Rapid and simple taxonomic profiling of genome and metagenome contigs

• UpdatedJun 13, 2023
• Python

This project is created by the Hao Lab at the Chemistry Department in George Washington University, Washington, D.C. This project aims to provide contaminant protein FASTA and spectral libraries that can be universally applied to DDA and DIA proteomics and freely accessible for the proteomics community.

• UpdatedNov 24, 2024

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

• UpdatedFeb 6, 2023
• Python

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

• UpdatedJul 29, 2013
• C

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

• UpdatedApr 30, 2018
• Python

Benchmarking different ways of doing read (taxonomic) classification, with a focus on removal of contamination and MTB classification

• UpdatedApr 8, 2024
• Python

Conta is an R package to detect cross contamination and source of contamination

• UpdatedFeb 25, 2020
• R

Analytical solutions for groundwater contaminant transport

• UpdatedAug 12, 2024
• Julia

DecontaMiner is a tool designed and developed to investigate the presence of contaminating sequences in unmapped NGS data. It can suggest the presence of contaminating organisms in sequenced samples, that might derive either from laboratory contamination or from their biological source, and in both cases can be considered as worthy of further in…

• UpdatedOct 12, 2024
• Perl