contamination
There are 1 repository under contamination topic.
DRL / blobtools
Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets
Language:Python 175benjjneb / decontam
Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
Language:R 137Griffan / VerifyBamID
VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.
Language:mupad 89- recentrifuge
khyox / recentrifuge
Recentrifuge: robust comparative analysis and contamination removal for metagenomics
Language:Python 85 - lm-contamination
hitz-zentroa / lm-contamination
The LM Contamination Index is a manually created database of contamination evidences for LMs.
Language:Python 71 - FastQ-Screen
StevenWingett / FastQ-Screen
Detecting contamination in NGS data and multi-species analysis
Language:HTML 54 - RawHash
CMU-SAFARI / RawHash
RawHash is the first mechanism that can accurately and efficiently map raw nanopore signals to large reference genomes (e.g., a human reference genome) in real-time without using powerful computational resources (e.g., GPUs). Described by Firtina et al. (published at https://academic.oup.com/bioinformatics/article/39/Supplement_1/i297/7210440)
Language:C 38 - Language:Java 29
Arkadiy-Garber / SprayNPray
Rapid and simple taxonomic profiling of genome and metagenome contigs
Language:Python 26HaoGroup-ProtContLib / Protein-Contaminant-Libraries-for-DDA-and-DIA-Proteomics
This project is created by the Hao Lab at the Chemistry Department in George Washington University, Washington, D.C..(Publication pending) 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.
mpieva / mapping-iterative-assembler
Consensus calling (or "reference assisted assembly"), chiefly of ancient mitochondria
Language:C 15htafer / remoVecSec
Module and script to remove contamination in assembled genomes before submission to ncbi
Language:Python 14pirovc / grimer
GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and metadata with focus on contamination detection.
Language:Python 13- Language:R 9
- decontaminer
amarinderthind / decontaminer
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 investigation and experimental validation. The novelty of DecontaMiner is mainly represented by its easy integration with the standard procedures of NGS data analysis, while providing a complete, reliable, and automatic pipeline. https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2684-x
Language:Perl 8 jnarayan81 / Alienomics
Automated pipeline for HGT and contaminant detection in an assembled, annotated genome
Language:Perl 8- Language:Julia 8
mbhall88 / classification_benchmark
Benchmarking different ways of doing read (taxonomic) classification, with a focus on removal of contamination and MTB classification
Language:Python 8- Language:Rust 8
- Language:Python 4
caravagnalab / TINC
Tumour-in-Normal Contamination assessment with evolutionary theory.
Language:R 4oslugr / contaminAND
Repositorio para análisis y publicación de datos de contaminación en Andalucía
Language:HTML 4RhettRautsaw / MitoSIS
MitoSIS (Mitochondrial Species Identification System) is a wrapper for mitochondrial genome assembly and identification of sample contamination or mislabeling.
Language:Python 4IARCbioinfo / conpair-nf
Nextflow pipeline for Conpair (concordance and contamination estimator)
Language:Nextflow 3- Language:Python 3
thanhtbt / aFAPI
[IEEE ICASSP 2023] "Robust Subspace Tracking with Contamination Mitigation via Alpha-Divergence". In 48th IEEE International Conference on Acoustics, Speech, & Signal Processing, 2023.
Language:MATLAB 3Reference-based, heuristic algorithm for identification of potential contaminants in mothur-formatted OTU tables
Language:Python 2open-stats-online / openucl_02
Shiny app for calculating & plotting data for UCL's and MK Trends
Language:HTML 2autoConTAMPR: Automatic Contingency Table Analysis of Minority Peak Ranks
Language:Perl 1PudinDeveloper / Sea-Sweepers
Godot educational game about oceans.
Language:GDScript 1mtdna / haplochecker
Contamination detection workflow based on mtDNA
0takashinedachi / Conductivity-monitoring-for-river
Water quality monitoring in river for pollution control applicating continuous conductivity monitoring. This is for evaluation of pollution level and its fluctuation as BOD5 converting by Conductivity value utilizing Arduino Nano.
Language:HTML 0Jason-Hargrove / project1
Escape if you can! A radiological event has occurred and you have to find your way out. Pick up items along the way that may help or harm you. When you've accumulate too much radiation it's game over.
Language:JavaScriptmadsjulia / MultizoneTransport.jl
Module simulating groundwater flow and contaminant transport in multiple groundwater zones (saturated and unsaturated)
Language:Julia- Language:R
valdiman / R-codes-for-East-Chicago-soil-PCB-analysis
R codes developed for East Chicago PCB soil paper. Codes describe how to create the maps and figures (ECSoilFigures.R), as well as all the statistical analyses (ECSoilStatTest.R) performed in the paper. All data are available and download from Pangaea. This is part of Project 6 of the ISRP (https://iowasuperfund.uiowa.edu/)
Language:R
