amplicon 开源项目推荐（73 个）

torognes /vsearch

多功能的开源微生物组分析工具

benjjneb /dada2

Accurate sample inference from amplicon data with single nucleotide resolution

benjjneb /decontam

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

nf-core /viralrecon

Assembly and intrahost/low-frequency variant calling for viral samples

lucapinello /CRISPResso

Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from sequencing data

microsud /Tools-Microbiome-Analysis

A list of R environment based tools for microbiome data exploration, statistical analysis and visualization

FOI-Bioinformatics /flextaxd

FlexTaxD（灵活分类数据库）——创建、添加、合并不同的分类源（QIIME、GTDB、NCBI 等）并创建宏基因组数据库（如 kraken2、ganon 等）

UPHL-BioNGS /Cecret

Reference-based consensus creation

gear-genomics /dicey

In-silico PCR, primer design and padlock design for in-situ sequencing

microsud /microbiomeutilities

The is mostly a wrapper tool using phyloseq and microbiome R packages.

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.

tobiasrausch /lorax

A long-read analysis toolbox for cancer and population genomics

mikessh /mageri

[DEPRECATED] MAGERI - Assemble, align and call variants for targeted genome re-sequencing with unique molecular identifiers

adrientaudiere /MiscMetabar

R package MiscMetabar: Miscellaneous functions for metabarcoding analysis

compmetagen /micca

micca - MICrobial Community Analysis

chienchi /amplicon_coverage_plot

interactive barplot for amplicon sequencing

HuaZou /bioinformatics_pipeline

Bioinformatics Pipeline

adriaaula /dada2_guidelines

A repository with a general dada2 pipeline for amplicon processing

gear-genomics /silica

In-silico PCR amplification on complete genomes

yanhui09 /laca

A reproducible and scalable workflow for Long Amplicon Consensus Analysis (LACA)