Amplicon sequencing data analysis bioinformatics software tools

Because of its low cost, amplicon sequencing, also known as ultra-deep targeted sequencing, is now becoming widely used in oncology for detection of actionable mutations, i.e. mutations influencing cell sensitivity to targeted therapies. Source text: Boeva et al., 2014.

Web app
G T A T C G C T A Amplicon Sequencing… Amplicon Sequencing Analysis Tools

AmpliSAT Amplicon Sequencing Analysis Tools

Performs analysis of amplicon sequencing results in a simple and efficient way,…

Performs analysis of amplicon sequencing results in a simple and efficient way, while offering customization options for advanced users. amplisas is designed as a three-step pipeline consisting of…

Desktop app
G T A T C G C T A MutAid MutAid

MutAid

A pipeline to analyze and interpret raw sequencing data produced by Sanger or…

A pipeline to analyze and interpret raw sequencing data produced by Sanger or several NGS sequencing platforms. MutAid performs format conversion, base calling, quality trimming, filtering, read…

Desktop app
G T A T C G C T A BaitFisher BaitFisher

BaitFisher

A software package for designing hybrid enrichment baits. BaitFisher consists…

A software package for designing hybrid enrichment baits. BaitFisher consists of two programs: BaitFisher and BaitFilter. The main goal of BaitFisher is to avoid redundancy in the construction of…

G T A T C G C T A Tumorsec Tumorsec

Tumorsec

A full workflow of NGS data analysis for detection of somatic mutations in a…

A full workflow of NGS data analysis for detection of somatic mutations in a clinical setting. We use ultra-deep targeted sequencing, producing fastq 4 files of about 150MB each per patient. Tumorsec…

Desktop app
G T A T C G C T A Bartender Bartender

Bartender

A clustering algorithm to detect barcodes and their abundances from raw…

A clustering algorithm to detect barcodes and their abundances from raw next-generation sequencing data. Bartender employs a divide-and-conquer strategy that intelligently sorts barcode reads into…

Desktop app
G T A T C G C T A targeted sequencing… targeted sequencing Support Vector Machine

tarSVM targeted sequencing Support Vector Machine

An open source variant filtering pipeline that uses a support vector machine…

An open source variant filtering pipeline that uses a support vector machine (SVM) and a new score the normalized allele dosage test to identify high quality variants from microfluidic PCR data.…

Desktop app
G T A T C G C T A PHYLUCE PHYLUCE

PHYLUCE

A package for phylogenomic analyses of data collected from conserved genomic…

A package for phylogenomic analyses of data collected from conserved genomic loci using targeted enrichment. PHYLUCE allows the assembly of raw read data to contigs, the identification of…

Desktop app
G T A T C G C T A Context-Aware Scheme… Context-Aware Scheme for Paired-End Reads

CASPER Context-Aware Scheme for Paired-End Reads

A computational method to rapidly and robustly merge overlapping paired-end…

A computational method to rapidly and robustly merge overlapping paired-end reads. CASPER uses quality scores and k-mer frequency for merging. When the difference between the quality scores of…

Desktop app
G T A T C G C T A ONCOCNV ONCOCNV

ONCOCNV

A method that includes a multifactor normalization and annotation technique…

A method that includes a multifactor normalization and annotation technique enabling the detection of large copy number changes from amplicon sequencing data. This approach was validated on high and…

Desktop app
G T A T C G C T A ROVER ROVER

ROVER

Enables users to quickly and accurately identify genetic variants from…

Enables users to quickly and accurately identify genetic variants from PCR-targeted, overlapping paired-end MPS datasets. The open-source availability of the software and threshold tailorability…

Desktop app
G T A T C G C T A quandico quandico

quandico

Applies statistical methods to detect copy number variations (CNV) in a sample…

Applies statistical methods to detect copy number variations (CNV) in a sample by comparing the read counts from next generation sequencing (NGS) performed after PCR-enrichment of regions of…

Curators for Amplicon sequencing analysis

  • Alvaro Sebastian's avatar image Alvaro Sebastian's country flag
    Alvaro Sebastian
    Evolutionary Biology Group,…

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