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Amplicon sequencing software tools

High-throughput sequencing 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., 2014Curator: Alvaro Sebastian

Amplicon Sequencing Analysis Tools

OMIC_10988

Amplicon Sequencing Analysis Tools
AmpliSAT

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

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 (i) read demultiplexing, (ii) unique sequence…

BaitFisher

OMIC_11740

BaitFisher

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

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 baits by designing fewer baits in conserved regions…

Context-Aware Scheme for Paired-End Reads

OMIC_07421

Context-Aware Scheme for Paired-End Reads
CASPER

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

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 mismatching base is significant, CASPER relies on the…

MutAid

OMIC_12003

MutAid

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

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 mapping, variant calling, variant annotation and…

ONCOCNV

OMIC_07427

ONCOCNV

A method that includes a multifactor normalization and annotation technique enabling the…

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 low amplicon density datasets and demonstrated…

PHYLUCE

OMIC_10301

PHYLUCE

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

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 ultra-conserved elements (UCE) contigs, parallel alignment…

quandico

OMIC_07419

quandico

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

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 interest, typically a set of genes with known or expected…

ROVER

OMIC_07420

ROVER

Enables users to quickly and accurately identify genetic variants from PCR-targeted,…

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 enables broad access for a range of PCR-MPS users.

Tumorsec

OMIC_10956

Tumorsec

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

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 generates several reports of tables and figures.…