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.

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AmpliSAT
Web

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…

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MutAid
Desktop
Virtual

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…

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BaitFisher
Desktop

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…

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Tumorsec
Docker

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…

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ampliQueso
Desktop

ampliQueso

Provides tools and reports for the analysis of amplicon sequencing panels, such…

Provides tools and reports for the analysis of amplicon sequencing panels, such as AmpliSeq. AmpliQueso is a machine learning classifier evaluation of the answer to the question of difference between…

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Bartender
Desktop

Bartender

Detects barcodes and their abundances from raw next-generation sequencing data.…

Detects barcodes and their abundances from raw next-generation sequencing data. Bartender employs a divide-and-conquer strategy that intelligently sorts barcode reads into distinct bins before…

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tarSVM
Desktop

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.…

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PHYLUCE
Desktop

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…

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CASPER
Desktop

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…

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ONCOCNV
Desktop

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…

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ROVER
Desktop

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…

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quandico
Desktop

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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