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GATK / Genome Analysis ToolKit
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Focuses on variant discovery and genotyping. GATK provides a toolkit, developed at the Broad Institute, composed of several tools and ables to support projects of any size. The application compiles an assortment of command line allowing one to analyze of high-throughput sequencing (HTS) data in various formats such as SAM, BAM, CRAM or VCF. The website includes multiple documentation for guiding users.
SAMtools
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Allows users to interact with high-throughput sequencing data. SAMtools permits the manipulation of alignments in the SAM/BAM/CRAM formats: reading, writing, editing, indexing, viewing and converting SAM/BAM/CRAM format. It limits the mapping quality of reads with excessive mismatches and applies base alignment quality to fix alignment errors. This tool can sort and merge alignments, remove polymerase chain reaction (PCR) duplicates or generate per-position information.
Syzygy
Implements methods for the analysis of pooled sequencing data generation. Syzygy is a variant calling method allowing: (i) single nucleotide polymorphism (SNP) calling on pooled data, (ii) estimation of allele frequencies of discovered variants, (iii) application of single-marker association test in pooled setting, (iv) group wise testing of rare and low frequency variants discovered, (v) power evaluation and quality control (QC) summary, as well as (vi) annotation of variants discovered in regions from primary sequencing data in BAM/SAM format.
Nanopolish
Provides a nanopore consensus algorithm using a signal-level hidden Markov model (HMM). The main subprograms of Nanopolish are: (i) nanopolish extract which extracts reads in FASTA or FASTQ format from a directory of FAST5 files; (ii) nanopolish eventalign which aligns signal-level events to k-mers of a reference genome; (iii) nanopolish variants which detects single nucleotide polymorphisms (SNPs) and indels with respect to a reference genome; and (iv) nanopolish variants –consensus which calculates an improved consensus sequence for a draft genome assembly. Furthermore, Nanopolish contains an experimental option that will use event durations to improve the consensus accuracy around homopolymers.
BLAT / BLAST-Like Alignment Tool
Finds genomic sequences that match a protein or DNA sequence submitted by the user. BLAT is a very fast sequence alignment tool similar to BLAST typically used for searching similar sequences within the same or closely related species. It was developed to align millions of expressed sequence tags and mouse whole-genome random reads to the human genome at a higher speed. BLAT is commonly used to look up the location of a sequence in the genome or determine the exon structure of an mRNA, but expert users can run large batch jobs and make internal parameter sensitivity changes by installing command line it on Linux server.
VarScan
A platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments. The newest version, VarScan 2, is written in Java, so it runs on most operating systems. It can be used to detect different types of variation: 1) germline variants (SNPs and indels) in individual samples or pools of samples, 2) multi-sample variants (shared or private) in multi-sample datasets (with mpileup), 3) somatic mutations, LOH events, and germline variants in tumor-normal pairs and 4) somatic copy number alterations (CNAs) in tumor-normal exome data.
Scalpel
A software package for detecting INDELs (INsertions and DELetions) mutations in a reference genome which has been sequenced with next-generation sequencing technology (e.g., Illumina). Scalpel is designed to perform localized micro-assembly of specific regions of interest with the goal of detecting mutations with high accuracy and increased power. Scalpel supports three modes of operation: single, de novo, and somatic. In the single mode, Scalpel detects indels in one single dataset (e.g., one individual exome). In the de novo mode, Scalpel detects de novo indels in a quad family (father, mother, affected child, unaffected sibling). In the somatic mode, Scalpel detects somatic indels from the sequencing data coming from matched tumor and normal samples.
DNAscan
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Offers a platform dedicated to DNA next-generation sequencing (NGS) data analysis, annotation and visualization. DNAscan can be set for running on various mode to adapt its performance to focus on a specific subregion or material. The application is able to detect a wide range of genetic material including single nucleotides variants (SNVs), repeat expansions and structural variants (SVs). The application can be run through Docker and Singularity.
Strelka
Provides analysis of germline variation in small cohorts and somatic variation in tumor/normal sample pairs. Strelka is a variant calling method building upon the innovative Strelka somatic variant caller to improve upon aspects of variant calling for both germline and somatic analysis. The germline caller employs an efficient tiered haplotype model to improve accuracy and provide read-backed phasing, adaptively selecting between assembly and a faster alignment-based haplotyping approach at each variant locus. The germline caller also analyzes input sequencing data using a mixture-model indel error estimation method to improve robustness to indel noise.
CRISP / Comprehensive Read analysis for Identification of Single Nucleotide Polymorphisms
Detects SNPs and short indels from high-throughput sequencing of pooled DNA samples. CRISP has been primarily developed to analyze data from "artificial" DNA pools, i.e. pools generated by equi-molar pooling of DNA from multiple individual samples. CRISP leverages sequence data from multiple such pools to detect both rare and common variants. Note that the method is not designed for variant detection from a single pool. CRISP was developed for targeted disease association studies in humans but may work well for other applications.
Dindel
A Bayesian method to call indels from short-read sequence data in individuals and populations by realigning reads to candidate haplotypes that represent alternative sequence to the reference. The candidate haplotypes are formed by combining candidate indels and SNVs identified by the read mapper, while allowing for known sequence variants or candidates from other methods to be included. In our probabilistic realignment model we account for base-calling errors, mapping errors, and also, importantly, for increased sequencing error indel rates in long homopolymer runs.
MATE-CLEVER / Mendelian-inheritance-AtTEntive CLique-Enumerating Variant finder
Detects genotype insertions and deletions from paired-end reads. CTK is a suite of tools for next-generation sequencing (NGS) data analysis and is based on an internal segment size approach to discover indel variation from paired-end read data. It contains also, among others, a long-indel-aware read mapper (LASER), a BAM converter to a list of alignment pairs with prior probabilities and a split feature by chromosome.
HySA / Hybrid Structural variant Assembly
Integrates sequencing reads from next-generation sequencing (NGS) and single-molecule sequencing (SMS) technologies to accurately assemble and detect structural variations (SV) in human genome. By identifying homologous SV-containing reads from different technologies through a bipartite-graph-based clustering algorithm, our approach turns a whole genome assembly problem into a set of independent SV assembly problems, each of which can be effectively solved to enhance assembly of structurally altered regions in human genome.
SvABA / Structural variation and indel Analysis By Assembly
Detects structural variants (SVs) from short-read sequencing data using genome-wide local assembly with low memory and computing requirements. SvABA’s performance was evaluated on the NA12878 human genome and in simulated and real cancer genomes. SvABA demonstrates superior sensitivity and specificity across a large spectrum of SVs, and substantially improved detection performance for variants in the 20-300 bp range, compared with existing methods. SvABA also identifies complex somatic rearrangements with chains of short (< 1,000 bp) templated-sequence insertions copied from distant genomic regions. SvABA was applied to 344 cancer genomes from 11 cancer types, and found that templated-sequence insertions occur in approximately 4% of all somatic rearrangements. Finally, SvABA can identify sites of viral integration and cancer driver alterations containing medium-sized SVs.
SomaticSeq
An accurate somatic mutation detection pipeline implementing a stochastic boosting algorithm to produce highly accurate somatic mutation calls for both single nucleotide variants and small insertions and deletions. The workflow currently incorporates five state-of-the-art somatic mutation callers, and extracts over 70 individual genomic and sequencing features for each candidate site. A training set is provided to an adaptively boosted decision tree learner to create a classifier for predicting mutation statuses.
Octopus-toolkit
Examines epigenomic and transcriptomic next generation sequencing (NGS) data. Octopus-toolkit can be used for antibody- or enzyme-mediated experiments and studies for the quantification of gene expression. It can accelerate the data mining of public epigenomic and transcriptomic NGS data for basic biomedical research. This tool provides a private and a public mode: one to process the user’s own data, and the other to analyze public NGS data by retrieving raw files from the GEO database.
BreakSeek
A breakpoint-based algorithm, which can unbiasedly and efficiently detect both homozygous and heterozygous INDELs, ranging from several base pairs to over thousands of base pairs, with accurate breakpoint and heterozygosity rate estimations. Comprehensive evaluations on both simulated and real datasets revealed that BreakSeek outperformed other existing methods on both sensitivity and specificity in detecting both small and large INDELs, and uncovered a significant amount of novel INDELs that were missed before.
bcftools
A statistical framework for calling SNPs, discovering somatic mutations, inferring population genetical parameters and performing association tests directly based on sequencing data. BCFtools can manipulate variant calls in the variant call format (VCF) and its binary counterpart BCF. It also can discover somatic and germline mutations with appropriate input data, efficiently estimate site allele frequency, allele frequency spectrum and linkage disequilibrium, and test Hardy–Weinberg equilibrium and association.
FermiKit
A variant calling pipeline for Illumina whole-genome germline data. It de novo assembles short reads and then maps the assembly against a reference genome to call SNPs, short insertions/deletions (INDELs) and structural variations (SVs). FermiKit takes about one day to assemble 30-fold human whole-genome data on a modern 16-core server with 85GB RAM at the peak, and calls variants in half an hour to an accuracy comparable to the current practice. FermiKit assembly is a reduced representation of raw data while retaining most of the original information.
PyroHMMvar
Calls single nucleotide polymorphisms (SNPs) and short indels for both Ion Torrent and 454 resequencing data. PyroHMMvar is a method that has two distinct features: (i) an HMM to formulate homopolymer errors and which can distinguish real signals from sequencing errors and thus improve the alignment of reads against the reference and (ii) a graph data structure that merges multiple aligned reads at a given locus into a weighted alignment graph. PyroHMMvar is also available as part of the toolkit PyroTools.
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 method is designed for rapid analysis on standard computer hardware: NA12878 at 50x genomic coverage is analyzed in less than 20 minutes on a 20 core server, most WGS tumor-normal analyses can be completed within 2 hours. Manta combines paired and split-read evidence during SV discovery and scoring to improve accuracy, but does not require split-reads or successful breakpoint assemblies to report a variant in cases where there is strong evidence otherwise. It provides scoring models for germline variants in individual diploid samples and somatic variants in matched tumor-normal sample pairs.
ScanIndel
Detects indels with multiple heuristics including gapped alignment, split reads and de novo assembly. Using simulation data, it was demonstrated ScanIndel’s superior sensitivity and specificity relative to several state-of-the-art indel callers across various coverage levels and indel sizes. ScanIndel yields higher predictive accuracy with lower computational cost compared with existing tools for both targeted resequencing data from tumor specimens and high coverage whole-genome sequencing (WGS) data from the human NIST standard NA12878. ScanIndel will improve indel analysis in both clinical and research settings. ScanIndel is implemented in Python, and is freely available for academic use.
16GT
Provides a variant caller for Illumina whole genome sequencing (WGS) and whole exome sequencing (WES) germline data. 16GT uses a new 16-genotype probabilistic model to unify single nucleotide polymorphism (SNP) and indel calling in a single variant calling algorithm. In benchmark comparisons with five other widely used variant callers on a modern 36-core server, 16GT ran faster and demonstrated improved sensitivity in calling SNPs, and it provided comparable sensitivity and accuracy in calling indels as compared to the GATK HaplotypeCaller.
SV-M / Structural Variant Machine
Detects indel candidates using a discriminative classifier based on features of split read alignment profiles and trained on true and false indel candidates that were validated by Sanger sequencing. SV-M is able to discover and distinguish true from false indel candidates in order to reduce the false positive rate. The key benefit of using a discriminative model is to learn to distinguish between true and false candidates based on a Sanger validated ground truth, thereby reducing the false positive rate among predicted indels.
INDELseek
Detects complex indels from next-generation sequencing (NGS) reads. INDELseek was demonstrated as an accurate and versatile complex indel caller, which is compatible with somatic and germline genomics studies, NGS data of random fragments and polymerase chain reaction (PCR) amplicons, and all three classes of complex indels (MNV, net insertion and net deletion). Since INDELseek was implemented as a single Perl script that directly reads SAM/BAM alignments and returns complex indel calls in VCF format, it can be readily incorporated into common bioinformatics workflows without any compilation and installation. INDELseek complements other common variant callers in academic and diagnostic NGS-based genomics studies.
CoVaCS / Consensus Variant Calling System
Enables genotyping and variant annotation of resequencing data produced by second generation next generation sequencing (NGS) technologies. CoVaCS is an automated system that provides tools for variant calling and annotation along with a pipeline for the analysis of whole genome shotgun (WGS), whole exome sequencing (WES) and targeted resequencing data (TGS). The software allows non-specialists to perform all steps from quality trimming to variant annotation.
GINDEL
An approach for calling genotypes of both insertions and deletions from sequence reads. GINDEL uses a machine learning approach which combines multiple features extracted from next generation sequencing data. It performs well for insertion genotyping on both simulated and real data. GINDEL can not only call genotypes of insertions and deletions (both short and long) for high and low coverage population sequence data, but also is more accurate and efficient than other approaches.
AMF / AgroMarker Finder
A GUI software for providing graphical user interface (GUI) to facilitate the recently developed restriction-site associated DNA (RAD) sequencing data analysis in rice. AMF integrates sophisticated tools with self-developed algorithms that can help users finish data analysis with simple operation. It consists of five independent modules: FilterAndMapping, BamConvert, NPInDel, DetectionAndAnnotation, SomaticDetection and VariantLocation. Based on this software, large volumes of polymorphism data have been discovered and analyzed, which will be meaningful for further application, such as genetic mapping, genetic map construction, evolutionary studies and marker-assisted seletion.
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