Here are
39 public repositories
matching this topic...
Versatile open-source tool for microbiome analysis
Accurate sample inference from amplicon data with single nucleotide resolution
Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from sequencing data
Updated
May 17, 2019
Python
Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
A list of R environment based tools for microbiome data exploration, statistical analysis and visualization
Assembly and intrahost/low-frequency variant calling for viral samples
Updated
May 17, 2022
Nextflow
FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomic databases (kraken2, ganon and more )
Updated
May 3, 2022
Python
The is mostly a wrapper tool using phyloseq and microbiome R packages.
MAGERI - Assemble, align and call variants for targeted genome re-sequencing with unique molecular identifiers
micca - MICrobial Community Analysis
Updated
Feb 12, 2020
Python
Nextflow workflow for our analysis of SARS-COV-2
Updated
May 27, 2022
Nextflow
In-silico PCR and variant primer design
interactive barplot for amplicon sequencing
Updated
Dec 10, 2021
HTML
Automated virus amplicon sequencing analysis program integrated with Nextflow pipeline manager.
Updated
Mar 11, 2022
Nextflow
[BETA] De-multiplexing and UMI-based consensus assembly for a wide range of data types: amplicon-seq, exome-seq, RNA-Seq, scRNA-Seq. Free for academic use only, contact
https://milaboratory.com .
Updated
Nov 27, 2020
Java
A long-read analysis toolbox for cancer genomics
extract long read subsequences from a pair of primers
Updated
Feb 11, 2022
Shell
MegaPath: sensitive and rapid pathogen detection using metagenomic NGS data; MegaPath-Amplicon: filtering module for metagenomic amplicon data
Updated
Feb 10, 2022
Java
In-silico PCR amplification on complete genomes
Updated
Apr 26, 2022
JavaScript
Reproducible Scalable Pipeline For Amplicon-based Metagenomics (RSP4ABM) is a bioinformatic pipeline designed for convenient, reproducible and scalable amplicon-based metagenomics
A repository with a general dada2 pipeline for amplicon processing
A unified framework for molecular inversion probe and amplicon analysis. Provides the tools to parse, manipulate, analyze, and visualize data.
Some tools made along the way when analyzing 16S amplicon data and metagenomics processing code
Updated
Aug 17, 2018
Jupyter Notebook
process raw reads from ubiome
Updated
Aug 6, 2018
Python
Reference-based, heuristic algorithm for identification of potential contaminants in mothur-formatted OTU tables
Updated
Apr 20, 2021
Python
A python package to process UMI tagged mixed amplicon metabarcoding data.
Updated
Mar 20, 2021
Python
Targeted characterisation of short structural variation.
Updated
Jan 12, 2022
Python
R functions and workflow for submitting amplicon sequence data to the ENA.
A unified searchable database of 16S rRNA amplicon libraries
Updated
Oct 14, 2018
Python
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