contamination

There are 46 repositories under contamination topic.

  • DRL/blobtools

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

    Language:Python195910444

  • benjjneb/decontam

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

    Language:R1501215125

  • Griffan/VerifyBamID

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

    Language:mupad9485515
  • recentrifuge

    khyox/recentrifuge

    Recentrifuge: robust comparative analysis and contamination removal for metagenomics

    Language:Python866527
  • lm-contamination

    hitz-zentroa/lm-contamination

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

    Language:Python76534
  • FastQ-Screen

    StevenWingett/FastQ-Screen

    Detecting contamination in NGS data and multi-species analysis

    Language:HTML6755817
  • RawHash

    CMU-SAFARI/RawHash

    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 at https://academic.oup.com/bioinformatics/article/39/Supplement_1/i297/7210440).

    Language:C508105

  • mbhall88/nohuman

    Remove human reads from a sequencing run

    Language:Rust34113

  • seppinho/mutserve

    mtDNA Variant Caller

    Language:Java3310406

  • Arkadiy-Garber/SprayNPray

    Rapid and simple taxonomic profiling of genome and metagenome contigs

    Language:Python27485

  • Plant-Food-Research-Open/assemblyqc

    A Nextflow pipeline for evaluating assembly quality

    Language:Nextflow27131265

  • HaoGroup-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. 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.

    23123

  • 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.

    Language:Python22253

  • mpieva/mapping-iterative-assembler

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

    Language:C16437

  • htafer/remoVecSec

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

    Language:Python14430

  • mbhall88/classification_benchmark

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

    Language:Python1120

  • grailbio/conta

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

    Language:R101417
  • 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:Perl9370

  • jnarayan81/Alienomics

    Automated pipeline for HGT and contaminant detection in an assembled, annotated genome

    Language:Perl9130

  • madsjulia/Anasol.jl

    Analytical solutions for groundwater contaminant transport

    Language:Julia9904

  • microsoft/private-benchmarking

    A platform that enables users to perform private benchmarking of machine learning models. The platform facilitates the evaluation of models based on different trust levels between the model owners and the dataset owners.

    Language:Python7311

  • CamilaDuitama/decOM

    🗑️🦷 decOM 🦷🗑️

    Language:Python5422

  • caravagnalab/TINC

    Tumour-in-Normal Contamination assessment with evolutionary theory.

    Language:R5362

  • oslugr/contaminAND

    Repositorio para análisis y publicación de datos de contaminación en Andalucía

    Language:HTML49510

  • RhettRautsaw/MitoSIS

    MitoSIS (Mitochondrial Species Identification System) is a wrapper for mitochondrial genome assembly and identification of sample contamination or mislabeling.

    Language:Python4221

  • castro-gzlz/TESS-cont

    Flux contamination analysis (TESS)

    Language:Jupyter Notebook31

  • IARCbioinfo/conpair-nf

    Nextflow pipeline for Conpair (concordance and contamination estimator)

    Language:Nextflow360

  • johrollin/Cont_ID

    cross-contamination of plant virus base on read assignation

    Language:Python3100

  • 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:MATLAB3102

  • Arkadiy-Garber/Taxonsluice

    Reference-based, heuristic algorithm for identification of potential contaminants in mothur-formatted OTU tables

    Language:Python2101

  • open-stats-online/openucl_02

    Shiny app for calculating & plotting data for UCL's and MK Trends

    Language:HTML2000

  • andreaponti5/waco

    Simulate the diffusion of contaminants in water networks.

    Language:Python1100

  • jnarayan81/autoConTAMPR

    autoConTAMPR: Automatic Contingency Table Analysis of Minority Peak Ranks

    Language:Perl1210

  • madsjulia/MultizoneTransport.jl

    Module simulating groundwater flow and contaminant transport in multiple groundwater zones (saturated and unsaturated)

    Language:Julia1401

  • pemori/S-DSS

    Codes for a geoSpatial Decision Support Systems (S-DSS) for sustainable land use. Article published in Land Degradation & Development (2024)

    Language:R1100

  • PudinDeveloper/Sea-Sweepers

    Godot educational game about oceans.

    Language:GDScript1101