chienchi/amplicon_coverage_plot

interactive barplot for amplicon sequencing

Language: HTML - Size: 6.09 MB - Last synced at: 2 days ago - Pushed at: 5 months ago - Stars: 14 - Forks: 5

UPHL-BioNGS/Cecret

Reference-based consensus creation

Language: Nextflow - Size: 277 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 53 - Forks: 27

torognes/vsearch

Versatile open-source tool for microbiome analysis

Language: C++ - Size: 8.4 MB - Last synced at: 14 days ago - Pushed at: 18 days ago - Stars: 695 - Forks: 127

benjjneb/dada2

Accurate sample inference from amplicon data with single nucleotide resolution

Language: R - Size: 468 MB - Last synced at: 20 days ago - Pushed at: 3 months ago - Stars: 489 - Forks: 146

ess-dive-workspace/essdive-amplicon

READY TO USE. Repository containing guidelines and templates for archiving amplicon sequencing data with ESS-DIVE repository.

Size: 376 KB - Last synced at: 18 days ago - Pushed at: 28 days ago - Stars: 0 - Forks: 1

CassandraHjo/Rsearch

Rsearch is an R package designed for handling and analyzing targeted sequencing data.

Language: R - Size: 8.81 MB - Last synced at: 30 days ago - Pushed at: 30 days ago - Stars: 0 - Forks: 0

tobiasrausch/lorax

A long-read analysis toolbox for cancer and population genomics

Language: C++ - Size: 203 KB - Last synced at: 12 days ago - Pushed at: 2 months ago - Stars: 22 - Forks: 1

wenjie1991/CellBarcode

R package for cellular DNA barcode data preprocessing.

Language: R - Size: 9.54 MB - Last synced at: 7 days ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 1

adrientaudiere/MiscMetabar

R package MiscMetabar: Miscellaneous functions for metabarcoding analysis

Language: R - Size: 334 MB - Last synced at: 4 days ago - Pushed at: 16 days ago - Stars: 17 - Forks: 0

adriaaula/dada2_guidelines

A repository with a general dada2 pipeline for amplicon processing

Language: R - Size: 80.8 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 9 - Forks: 5

FOI-Bioinformatics/flextaxd

FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomic databases (kraken2, ganon and more )

Language: Python - Size: 1.06 MB - Last synced at: 11 days ago - Pushed at: about 1 month ago - Stars: 65 - Forks: 8

BostonGene/pyigmap

[UNDER DEVELOPMENT] Pipeline for mapping and annotating T- and B-cell receptor gene rearrangement sequences

Language: Python - Size: 17.2 MB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 3 - Forks: 0

lucapinello/CRISPResso 📦

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

Language: Python - Size: 4.93 MB - Last synced at: 4 days ago - Pushed at: almost 6 years ago - Stars: 135 - Forks: 57

yanhui09/laca

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

Language: Python - Size: 124 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 7 - Forks: 2

metagenlab/zAMP

zAMP is a bioinformatic pipeline designed for convenient, reproducible and scalable amplicon-based metagenomics

Language: R - Size: 198 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 8 - Forks: 5

angelovangel/nxf-tgs

Process raw Oxford Nanopore data, generate html report, and do de novo assembly (plasmid, amplicon, bacterial genome)

Language: R - Size: 159 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

gear-genomics/dicey

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

Language: C++ - Size: 384 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 47 - Forks: 4

quadram-institute-bioscience/phylobarcode

<pilot> in-silico amplicons optimised for phylogenetic signal

Language: Python - Size: 563 KB - Last synced at: 5 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

nf-core/viralrecon

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

Language: Nextflow - Size: 9.84 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 121 - Forks: 108

gear-genomics/silica

In-silico PCR amplification on complete genomes

Language: JavaScript - Size: 1.57 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 9 - Forks: 0

Nucleomics-VIB/InSilico_PCR

extract long read subsequences from a pair of primers

Language: Shell - Size: 22.4 MB - Last synced at: 9 months ago - Pushed at: about 3 years ago - Stars: 5 - Forks: 1

Aveglia/vAMPirus

Automated virus amplicon sequencing analysis program integrated with Nextflow pipeline manager.

Language: Nextflow - Size: 28 MB - Last synced at: about 1 month ago - Pushed at: 11 months ago - Stars: 9 - Forks: 3

sebrauschert/OceanOmics-amplicon

A pipeline to analyse marine fish amplicon data

Language: R - Size: 42.2 MB - Last synced at: 11 months ago - Pushed at: over 1 year ago - Stars: 4 - Forks: 2

microsud/Tools-Microbiome-Analysis

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

Language: CSS - Size: 6.07 MB - Last synced at: 11 months ago - Pushed at: about 2 years ago - Stars: 109 - Forks: 46

robiwangriff/ENA-submission-in-R

R functions and workflow for submitting amplicon sequence data to the ENA.

Language: R - Size: 246 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 1

benjjneb/decontam

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

Language: R - Size: 1.25 MB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 133 - Forks: 23

microsud/microbiomeutilities

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

Language: R - Size: 40 MB - Last synced at: 11 months ago - Pushed at: over 2 years ago - Stars: 32 - Forks: 7

compmetagen/micca

micca - MICrobial Community Analysis

Language: Python - Size: 5.02 MB - Last synced at: about 1 month ago - Pushed at: about 5 years ago - Stars: 20 - Forks: 9

yjiakang/amplicon

amplicon pipeline

Language: Shell - Size: 5.13 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

mikessh/mageri

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

Language: Java - Size: 99.7 MB - Last synced at: over 1 year ago - Pushed at: almost 8 years ago - Stars: 19 - Forks: 6

Majid-Soheili/BMDSRA

Sequence Read Archive Classification

Language: Python - Size: 44.7 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 1

yanhui09/nart

A tool for Nanopore Amplicon Real-Time (NART) analysis.

Language: Python - Size: 46.9 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

HKU-BAL/MegaPath

MegaPath: sensitive and rapid pathogen detection using metagenomic NGS data; MegaPath-Amplicon: filtering module for metagenomic amplicon data

Language: Java - Size: 23.2 MB - Last synced at: 7 days ago - Pushed at: about 3 years ago - Stars: 6 - Forks: 0

arriam-lab2/misal

A unified searchable database of 16S rRNA amplicon libraries

Language: Python - Size: 703 KB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 1

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: Python - Size: 5.37 MB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 11 - Forks: 2

HuaZou/bioinformatics_pipeline

Bioinformatics Pipeline

Language: R - Size: 5.73 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 9 - Forks: 9

natmurad/amplicon16S

Analysis for amplicon data

Language: Jupyter Notebook - Size: 134 KB - Last synced at: almost 2 years ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0

OpenOmics/DeepSeq

Ultra Deep Amplicon Sequencing Analysis of NPM1 gene

Language: Python - Size: 54.7 KB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

rwst/process-ubiome-16S 📦

process raw reads from ubiome

Language: Python - Size: 10.7 KB - Last synced at: about 2 years ago - Pushed at: over 6 years ago - Stars: 2 - Forks: 0

myonaung/Probe-Maker

Probe-Maker is intended for design of hybridisation probes for Plasmodium falciparum for long-read amplicon sequencing.

Size: 822 KB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

jfjlaros/tssv

Targeted characterisation of short structural variation.

Language: Python - Size: 243 KB - Last synced at: 7 days ago - Pushed at: over 3 years ago - Stars: 2 - Forks: 1

JasperBoom/caltha

A python package to process UMI tagged mixed amplicon metabarcoding data.

Language: Python - Size: 2.2 MB - Last synced at: 18 days ago - Pushed at: about 4 years ago - Stars: 2 - Forks: 1

bailey-lab/miplicorn

A unified framework for molecular inversion probe and amplicon analysis. Provides the tools to parse, manipulate, analyze, and visualize data.

Language: R - Size: 9.93 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 3 - Forks: 2

sabahzero/Puerto-Nuevo_Coastal-Microbial-Ecology_16S-18S-Workflow_UlHasan-etal

This is a microbial amplicon sequence (16S and 18S iTag) data and analyses pipeline corresponding to the manuscript, "Community ecology across bacteria, archaea and microbial eukaryotes in the sediment and seawater of coastal Puerto Nuevo, Baja California" for public benefit and usage.

Size: 1.02 MB - Last synced at: about 1 year ago - Pushed at: almost 6 years ago - Stars: 1 - Forks: 0

Arkadiy-Garber/Taxonsluice

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

Language: Python - Size: 9.99 MB - Last synced at: over 1 year ago - Pushed at: about 4 years ago - Stars: 2 - Forks: 1

ebete/amplicon-qtl

Mirror of amplicon-qtl repository.

Language: R - Size: 35.2 KB - Last synced at: about 2 years ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 0

ebete/micro-qtl

Mirror of micro-qtl repository.

Language: Python - Size: 84 KB - Last synced at: about 2 years ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0

Junyu25/PCAS

PCAS: check the coverage of your primer pair before putting on amplicon sequencing

Language: Python - Size: 186 KB - Last synced at: 9 months ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

pjtorres/16S_amplicon_preprocessing_code

Some tools made along the way when analyzing 16S amplicon data and metagenomics processing code

Language: Jupyter Notebook - Size: 3.58 MB - Last synced at: about 2 years ago - Pushed at: over 6 years ago - Stars: 2 - Forks: 0

fedarko/ampliviz

Visualizes breakpoint graphs generated by AmpliconArchitect; simulates the effects of long read data on the graph

Language: Python - Size: 59.6 KB - Last synced at: about 1 month ago - Pushed at: about 6 years ago - Stars: 0 - Forks: 0

romunov/MID_UMI Fork of sand60/MID_UMI

Accel Amplicon HS wMID

Language: Shell - Size: 1.66 MB - Last synced at: about 2 years ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0

tycheleturner/pacbio

Size: 3.91 KB - Last synced at: almost 2 years ago - Pushed at: about 8 years ago - Stars: 0 - Forks: 0

LordGenome/amplivar

Grouped Read Testing

Language: Perl - Size: 25.2 MB - Last synced at: over 1 year ago - Pushed at: about 8 years ago - Stars: 0 - Forks: 1