GitHub topics: contamination-detection
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 - Size: 1.45 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 9 - Forks: 0
KulikDM/pythresh
Outlier Detection Thresholding
Language: Jupyter Notebook - Size: 14.8 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 132 - Forks: 6
metagenopolis/CroCoDeEL
CroCoDeEL is a tool that detects cross-sample contamination in shotgun metagenomic data
Language: Python - Size: 2.72 MB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 24 - Forks: 0
WayneGitShell/GWSDAT
GroundWater Spatiotemporal Data Analysis Tool (GWSDAT) R-Shiny implementation.
Language: R - Size: 69.7 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 33 - Forks: 7
phac-nml/mikrokondo
A simple pipeline for bacterial assembly and quality control
Language: Nextflow - Size: 14.4 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 17 - Forks: 3
msk-access/biometrics
Python package to calculate various sample contamination metrics.
Language: Python - Size: 3.83 MB - Last synced at: 29 days ago - Pushed at: about 2 months ago - Stars: 8 - Forks: 2
Gabriel-Machado-GM/Study-of-linear-algebra-Contagion-and-Diseases
Epidemic Modeling Study: This study analyzes with Linear Algebra the progression of disease contagion within a population. Covid-19 Dashboard: We have created an interactive dashboard to analyze the data on the behavior of the Coronavirus in Brazil. The project is powered by a public CSV dataset.
Language: Python - Size: 2.49 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 2 - Forks: 0
scholl-lab/plasmicheck
Detect and quantify plasmid DNA contamination in sequencing data
Language: Python - Size: 116 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0
auroramaurizio/my_DNA_seq_pipelines
In this repository I backup the pipelines I write for the project I am involved
Language: Python - Size: 2.85 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0
raymondkiu/bactspeciesID
Fast microbial species identification (16S rRNA gene-based approach) and contamination check using whole genome assemblies
Language: Shell - Size: 77.1 KB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 2
alipirani88/QC-d
Generate Coverage, Quality and Contamination metrics for Sequence data.
Language: Jupyter Notebook - Size: 16.1 MB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 2 - Forks: 2
jfisbein/luftdaten
luftdaten script for raspberry with enviro+
Language: Python - Size: 316 KB - Last synced at: over 1 year ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 0
