High-throughput sequencing software tools > Whole-genome sequencing software tools
An algorithm for the correct alignment of two nucleotide sequences containing SVs, i.e.…
An algorithm for the correct alignment of two nucleotide sequences containing SVs, i.e. deletion, insertion, tandem duplication or inversion. The algorithm does not require the adjustment or modification of the alignment scoring scheme(s) that is…
Tools for insert site detection and for the assembly of novel insertions. BASIL features…
Tools for insert site detection and for the assembly of novel insertions. BASIL features an efficient sliding window implementation for clustering read alignments at insertion sites and clipping signals into a novel combination. ANISE allows for the…
A Perl/C++ package that provides genome-wide detection of structural variants from next…
A Perl/C++ package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. BreakDancer sensitively and accurately detected indels ranging from 10 base pairs to 1 megabase pair that are difficult…
An approach that uses a 'kmer' strategy to assemble misaligned sequence reads…
An approach that uses a 'kmer' strategy to assemble misaligned sequence reads for predicting insertions, deletions, inversions, tandem duplications and translocations at base-pair resolution in targeted resequencing data. Variants are…
A suite of programs that take aligned genomic data and report structural variation…
A suite of programs that take aligned genomic data and report structural variation breakpoints.
An internal segment size based approach, which organizes all, including concordant, reads…
An internal segment size based approach, which organizes all, including concordant, reads into a read alignment graph, where max-cliques represent maximal contradiction-free groups of alignments. An algorithm then enumerates all max-cliques and…
A tool for detecting structural variations with single-base resolution using…
A tool for detecting structural variations with single-base resolution using soft-clipping information.
An algorithm using NGS reads with partial alignments to a reference genome to directly…
An algorithm using NGS reads with partial alignments to a reference genome to directly map structural variations at the nucleotide level. Application of CREST to whole-genome sequencing data from five pediatric T-lineage acute lymphoblastic…
Hadoop-based structural variation (SV) caller for Illumina paired-end DNA sequencing data.
Hadoop-based structural variation (SV) caller for Illumina paired-end DNA sequencing data.
A tool for genome assembly and variation analysis from sequence data. You can use it to…
A tool for genome assembly and variation analysis from sequence data. You can use it to discover and genotype variants on single or multiple haploid or diploid samples. If you have multiple samples, you can use Cortex to look specifically for…
A sound generic multi-split SV detection tool that detects and classifies deletions,…
A sound generic multi-split SV detection tool that detects and classifies deletions, inversions, dispersed duplications and translocations of >/=30 bp.
A package for assembling genomes from Illumina short read sequence data. This package was…
A package for assembling genomes from Illumina short read sequence data. This package was used to assemble 18 accessions of A. thaliana. IMR/DENOM comprises three independent programs: IMR, DENOM and MCMERGE.
Detects and visualizes structural variation from paired-end mapping data. Under this…
Detects and visualizes structural variation from paired-end mapping data. Under this scheme, abnormally mapped read pairs are clustered based on the location of a gap signature. Several important features, including local depth of coverage, mapping…
Calls structural variants (SVs) and indels from mapped paired-end sequencing reads. Manta…
Calls structural variants (SVs) and indels from mapped paired-end sequencing reads. Manta is optimized for analysis of individuals and tumor/normal sample pairs, calling SVs, medium-sized indels and large insertions within a single workflow. The…
To characterize the mutational spectrum of somatic SVs in cancer, it is important to…
To characterize the mutational spectrum of somatic SVs in cancer, it is important to identify both simple (e.g., deletion, insertion, and inversion) and complex SVs at base-pair resolution. Meerkat predicts both germline and somatic SVs directly…
An approach that accurately discovers and genotypes indels longer than 30 bp from…
An approach that accurately discovers and genotypes indels longer than 30 bp from contemporary NGS reads with a special focus on family data. For enhanced quality of indel calls in family trios or quartets, MATE-CLEVER integrates statistics that…
An integrated structural variation (SV) caller which leverages multiple orthogonal SV…
An integrated structural variation (SV) caller which leverages multiple orthogonal SV signals for high accuracy and resolution. MetaSV proceeds by merging SVs from multiple tools for all types of SVs. It also analyzes soft-clipped reads from…
A software tool that performs detection and assembly of DNA insertion variants in NGS…
A software tool that performs detection and assembly of DNA insertion variants in NGS read datasets with respect to a reference genome. MindTheGap is designed to call insertions of any size, whether they are novel or duplicated, homozygous or…
It is designed to detect novel sequence insertions using high throughput paired-end whole…
It is designed to detect novel sequence insertions using high throughput paired-end whole genome sequencing data.
A method that identifies SVs and their precise breakpoints from whole-genome resequencing…
A method that identifies SVs and their precise breakpoints from whole-genome resequencing data. PRISM uses a split-alignment approach informed by the mapping of paired-end reads, hence enabling breakpoint identification of multiple SV types,…
Considers both intra-read discordance and soft-clipped tails of long reads (>10,000…
Considers both intra-read discordance and soft-clipped tails of long reads (>10,000 bp) to identify structural variants. As a proof of concept, we identify four structural variants and two genomic features in a strain of Escherichia coli with…
A computational framework with simulation-based error models for inferring genomic…
A computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. The package is composed of three modules, PEMer workflow, SV-Simulation and BreakDB. PEMer workflow is a…
Detects breakpoints of large deletions, medium sized insertions, inversions, tandem…
Detects breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-generation sequence data. Pindel uses a pattern growth approach to identify the…
A tool designed for efficient and accurate variant-detection in high-throughput…
A tool designed for efficient and accurate variant-detection in high-throughput sequencing data. By using local realignment of reads and local assembly it achieves both high sensitivity and high specificity. Platypus can detect SNPs, MNPs, short…
A method for discovering and genotyping novel sequence insertions. PopIns takes as input…
A method for discovering and genotyping novel sequence insertions. PopIns takes as input a reads-to-reference alignment, assembles unaligned reads using a standard assembly tool, merges the contigs of different individuals into high-confidence…
A program designed to process previously aligned, Illumina Paired-end whole genome…
A program designed to process previously aligned, Illumina Paired-end whole genome sequence data to identify structural variants such as deletions, insertions and tandem duplications. Simulations using RAPTR-SV and other, similar algorithms for SV…
Given paired-end mapped reads and a candidate high-copy region, Reprever identifies (a)…
Given paired-end mapped reads and a candidate high-copy region, Reprever identifies (a) the insertion breakpoints where the extra duplicons inserted into the donor genome and (b) the actual sequence of the duplicon. Reprever resolves ambiguous…
Detects structural variants from targeted short-DNA reads. Both real and simulated data…
Detects structural variants from targeted short-DNA reads. Both real and simulated data are used to demonstrate SLOPE's ability to rapidly detect insertion/deletion events of various sizes as well as translocations and viral integration sites…
A program for detecting the structural variation by whole genome de novo assembly System…
A program for detecting the structural variation by whole genome de novo assembly System Requirements.
A sensitive structural variant (SV) detection tool for Illumina paired-end…
A sensitive structural variant (SV) detection tool for Illumina paired-end next-generation sequencing data.
Detects structural variants in cancer using whole genome sequencing data with or without…
Detects structural variants in cancer using whole genome sequencing data with or without matched normal control sample. SV-Bay does not only use information about abnormal read mappings but also assesses changes in the copy number profile and tries…
Calculates annotations from one or more aligned bam files from many high-throughput…
Calculates annotations from one or more aligned bam files from many high-throughput sequencing technologies, and then builds a one-class model using these annotations to classify candidate structural variants (SVs) as likely true or false positives.…
A tool to detect genomic structural variations from paired-end and mate-pair sequencing…
A tool to detect genomic structural variations from paired-end and mate-pair sequencing data.
An improved approach for accurate and efficient calling of structural variations with…
An improved approach for accurate and efficient calling of structural variations with low-coverage sequence data.
A tool for discovery of structural variation in one or more individuals simultaneously…
A tool for discovery of structural variation in one or more individuals simultaneously using high throughput technologies. VariationHunter is now capable of resolving incompatible SV calls through a conflict resolution mechanism that no longer…
A comprehensive analysis platform for the processing, analysis and visualization of…
A comprehensive analysis platform for the processing, analysis and visualization of structural variation based on sequencing data or genomic microarrays, enabling the rapid identification of disease loci or genes. Vivar allows you to scale your…
