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:
(Boevaet al., 2014) Multi-factor data normalization enables the detection of copy number aberrations in amplicon sequencing data. Bioinformatics.
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…
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…
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…
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…
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…
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…
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…
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…
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…
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.…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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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