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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…
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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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COV'COP
Desktop

COV'COP

Aims to rapidly identify copy number variations (CNVs) responsible for…

Aims to rapidly identify copy number variations (CNVs) responsible for inherited diseases among amplicons sequencing data generated by next-generation sequencing (NGS). Cov'Cop simultaneously…

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TarSeqQC
Desktop

TarSeqQC

Permits quality control (QC) in Targeted Sequencing (TS) experiments after read…

Permits quality control (QC) in Targeted Sequencing (TS) experiments after read alignment and before variant calling analysis. TarSeqQC allows users to inquire specific and critical aspects, such as…

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MAGERI
Desktop

MAGERI Molecular tAgged GEnome Re-sequencing pIpeline

Allows to obtain high-fidelity mutation profiles and call ultra-rare variants…

Allows to obtain high-fidelity mutation profiles and call ultra-rare variants by handling caveats of Unique Molecular Identifier (UMI)-based analysis. MAGERI accounts for polymerase chain reaction…

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debarcer
Desktop

debarcer De-Barcoding and Error Correction

Facilitates the use of barcoded data generated by SiMSenSeq. Debarcer is a…

Facilitates the use of barcoded data generated by SiMSenSeq. Debarcer is a package for working with next-generation sequencing (NGS) data that contains molecular barcodes. It processes raw .fastq…

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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…

MPD
Web
Desktop

MPD Multiplex Primer Design

Automates the design of multiplex PCR primers for next-generation sequencing.…

Automates the design of multiplex PCR primers for next-generation sequencing. The core of MPD is implemented in C for speed and uses a hashed genome to ensure primer uniqueness, avoids placing…

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AmpliSAT
Web
Desktop

AmpliSAT Amplicon Sequencing Analysis Tools

Gathers a set of online tools that simplify the analysis of Amplicon Sequencing…

Gathers a set of online tools that simplify the analysis of Amplicon Sequencing experiments. AmpliSAT allows users to study Amplicon Sequencing (AS) that is a useful technique in the genotyping task…

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MutAid
Desktop

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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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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DUDE-Seq
Web
Desktop

DUDE-Seq Discrete Universal Denoiser-Sequence

Allows to denoise accurate DNA sequence. The DUDE algorithm was developed for a…

Allows to denoise accurate DNA sequence. The DUDE algorithm was developed for a general setting of reconstructing sequences with finite-valued components (source symbols) corrupted by a noise…

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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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BaitsTools
Desktop

BaitsTools

Facilitates baits’ designing and testing for hybridization capture.…

Facilitates baits’ designing and testing for hybridization capture. BaitsTools generates high-quality oligonucleotide baits from a wide range of formats from reference sequences or across the break…

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ThermoAlign
Desktop

ThermoAlign

Represents a genome-aware primer pair design algorithm. ThermoAlign is able to…

Represents a genome-aware primer pair design algorithm. ThermoAlign is able to use prior information on the locations of genomic variants during the selection of primer pairs. In order to design…

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BAMClipper
Desktop

BAMClipper

Removes gene-specific primer sequences from SAM/BAM alignments of polymerase…

Removes gene-specific primer sequences from SAM/BAM alignments of polymerase chain reaction (PCR) amplicons by soft-clipping. BAMClipper is an open-source, fast and effective tool to remove primers…

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ITDseek
Desktop

ITDseek

Improves the detection of FLT3-internal tandem duplication (ITD) of varying…

Improves the detection of FLT3-internal tandem duplication (ITD) of varying length, position and at low allelic burden. ITDseek is a FLT3-ITD detection algorithm that detects most false negatives (97…

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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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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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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…

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Tumorsec
Desktop

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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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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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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