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Bioinformatics workflow tools | Whole-genome sequencing data analysis

These software pipelines provide out-of-the box solutions for DNA sequencing analysis by chaining a number of specific analysis tools together.

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SpeedSeq
An open-source genome analysis platform that accomplishes alignment, variant detection and functional annotation of a 50× human genome in 13 h on a low-cost server and alleviates a bioinformatics bottleneck that typically demands weeks of computation with extensive hands-on expert involvement. SpeedSeq offers performance competitive with or superior to current methods for detecting germline and somatic single-nucleotide variants, structural variants, insertions and deletions, and it includes novel functionality for streamlined interpretation.
O-Miner
Allows automated analysis and annotation of complex -omics data. O-Miner is a solution for the analysis and exploitation of data. The software is composed of two analytical domains, genomics and transcriptomics, and a third analytical layer for the analysis of data from methylation arrays. Several established prostate cancer (PCa) biomarkers were identified using O-miner. It O-miner provides researchers with the tools required to conduct powerful analyses of publicly available sequencing data.
Crossbow
Searches for single nucleotide polymorphisms (SNPs) with cloud computing. Crossbow is a Hadoop-based software tool that combines the speed of the short read aligner Bowtie with the accuracy of the SNP caller SOAPsnp to perform alignment and SNP detection for multiple whole-human datasets per day. The software achieves at least 98.9% accuracy on simulated datasets of individual chromosomes, and better than 99.8% concordance with the Illumina 1 M BeadChip assay of a sequenced individual.
PyCogent / PYthon Comparative GENomic Toolkit
A framework to provide a collection of rigourously validated tools for the manipulation and analysis of genome biology data sets. PyCogent is a fully integrated and thoroughly tested framework for controlling third-party applications; devising workflows; querying databases; conducting novel probabilistic analyses of biological sequence evolution; and generating publication quality graphics. It is distinguished by many unique built-in capabilities (such as true codon alignment) and the frequent addition of entirely new methods for the analysis of genomic data.
NGSEP / Next Generation Sequencing Eclipse Plugin
Permits analysis of high throughput sequencing (HTS) data. NGSEP is an integrated framework whose main functionality is the variants detector, allowing researchers to make integrated discovery of single nucleotide variants (SNVs), small and large indels and regions with copy number variation (CNVs). The software also provides modules for read alignment, sorting, merging, functional annotation of variants, filtering and quality statistics.
GotCloud / Genomes on the Cloud
A pipeline for efficiently detecting and genotyping high-quality variants from large-scale sequencing data. GotCloud automates sequence alignment, sample-level quality control, variant calling, filtering of likely artifacts using machine-learning techniques, and genotype refinement using haplotype information. The pipeline can process thousands of samples in parallel and requires less computational resources than current alternatives. Experiments with whole-genome and exome-targeted sequence data generated by the 1000 Genomes Project show that the pipeline provides effective filtering against false positive variants and high power to detect true variants.
CLC bio / CLC Genomics Workbench
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Allows to analyze, compare, and visualize next generation sequencing (NGS) data. CLC Genomics Workbench offers a complete and customizable solution for genomics, transcriptomics, epigenomics, and metagenomics. The software enables to generate custom workflows, which can combine quality control steps, adapter trimming, read mapping, variant detection, and multiple filtering and annotation steps into a pipeline.
TOGGLE / TOolbox for Generic nGs anaLysEs
Enables users to design pipelines that manage large sets of next-generation sequencing (NGS) softwares and utilities. TOGGLE generates pipelines for largescale second- and third-generation sequencing analyses, including multi-threading support. It is designed for single nucleotide polymorphism (SNP) discovery for large sets of genomic data, ready to use in different environments (from a single machine to high performance computing (HPC) clusters).
NARWHAL
Automates the primary analysis of massive parallel sequencing data. NARWHAL is a sequence analysis pipeline that allows for the automated processing and analysis of different and multiplexed datasets obtained from Illumina sequencers and easy alignment of individual samples to the reference genome of choice using predefined alignment profiles. The software provides a coherent data analysis workflow with minimal hands-on time, a reduced chance of human error and faster analysis.
Pipeliner
Allows users to numerically measure the performance of different bioinformatics pipelines, which focus on the recovery and sensitivity in single nucleotide polymorphism (SNP) calling from resequencing data. Pipeliner consists of two separate executables: (1) a command-line tool used during the analysis to convert file formats and summarize the performance of the pipeline used; and (2) a graphical user interface (GUI) used for setting up the analysis parameters and plotting results.
Omics Pipe
A computational framework that automates multi-omics data analysis pipelines on high performance compute clusters and in the cloud. It supports best practice published pipelines for RNA-seq, miRNA-seq, Exome-seq, Whole Genome sequencing, ChIP-seq analyses and automatic processing of data from The Cancer Genome Atlas (TCGA). Omics Pipe provides researchers with a tool for reproducible, open source and extensible next generation sequencing analysis. The goal of Omics Pipe is to democratize NGS analysis by dramatically increasing the accessibility and reproducibility of best practice computational pipelines, which will enable researchers to generate biologically meaningful and interpretable results.
Aozan
Automatically handles data transfer, demultiplexing conversion and quality control once a HiSeq run has been finished. Aozan is an automated post sequencing data processing pipeline. It is a non-interactive program that consists of a suite of steps that are linked together from the detection of a new run launch to the creation of the quality control report once the run has finished. Once the software is configured, biologists can manage the entire sequencing process from library preparation to FASTQ generation and QC report.
Dugong
Allows automated installation of bioinformatics tools in computational environments. Dugong is a comprehensive Docker-based virtual desktop that integrates more than 3500 bioinformatics softwares using an XFCE4 Graphic User Interface (GUI). The desktop incorporates software’s available from three major open-source bioinformatics repositories: BioConda, LinuxBrew and BioLinux Repository. It also incorporates Jupyter Notebook and can be integrated into Dockstore pipelines by Common Workflow Language (CWL) and used to visualize graphical results from different types of analysis.
GIPS / Gene Identification via Phenotype Sequencing
A pipeline for sequencing-based direct gene cloning. GIPS considers a range of experimental and data analysis choices in a sequencing-based forward genetics study to design an optimal procedure for gene identification. GIPS estimates four measurements to help optimize an analysis procedure as follows: (i) the chance of reporting the true phenotype-associated gene, (ii) the expected number of random genes that may be reported, (iii) the significance of each candidate gene’s association with the phenotype, and (iv) the significance of violating the Mendelian assumption if no gene is reported or if all candidate genes have failed validation.
CALIN / Composable Asynchronous Logic using Integrase Networks
Serves as a scalable composition tool for implementing asynchronous Boolean logic within a multi-cellular consortium. CALIN consists of two main steps: it first decomposes the Boolean function of interest into a disjunction of conjunctive clauses via the Quine-McCluskey algorithm. The software then converts each clause into a given computational device for which particular connections are created between integrases and inputs.
GMS / Genome Modeling System
Detects, summarizes, visualizes, and interprets the various types of somatic and germline events encountered in variant analysis. GMS makes open, high-throughput genome analysis available to groups currently tasked to analyze the deluge of data from high-throughput sequencing (HTS) experiments. It also includes an integration, annotation, and interpretation pipeline, ‘MedSeq’, which attempts to converge all single-subject data into a form suitable for identification of clinically actionable events.
Chipster
Consists of a collection of investigation approaches and displays software for microarray data. Chipster is useful for several types of high throughput data such as microarrays, proteomics and next generation sequencing (NGS). It can be employed to normalize most of the commonly used chip types and permits to utilize the remapped information. This tool is useful for RNA degradation, relative log expression (RLE), normalized unscaled standard error (NUSE) or quality control probe expression.
QuickNGS
A workflow system for laboratories with the need to analyze data from multiple NGS projects at a time. QuickNGS takes advantage of parallel computing resources, a comprehensive back-end database, and a careful selection of previously published algorithmic approaches to build fully automated data analysis workflows. QuickNGS considerably reduces the barriers that still limit the usability of the powerful NGS technology and finally decreases the time to be spent before proceeding to further downstream analysis and interpretation of the data.
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.
miRPursuit
Allows analyses of high-throughput small RNA (sRNA) sequence data in model and non-model plants, from raw data to identified and annotated conserved and novel sequences. miRPursuit is a pipeline performing a series of sRNA analyses. The software minimizes the need to perform manual repetitive tasks allowing to run several libraries in parallel, for comparing differences in sRNA read accumulation among sRNA libraries. It can directly analyze the sRNA sequencing raw data from any sequencer.
PEPR / Pipelines for Evaluating Prokaryotic References
A reproducible and transparent bioinformatics tool for characterizing the reference genome of prokaryotic genomic materials. PEPR evaluates the quality, purity, and homogeneity of the reference material genome, and purity of the genomic material. The quality of the genome is evaluated using high coverage paired-end sequence data; coverage, paired-end read size and direction, as well as soft-clipping rates, are used to identify mis-assemblies. The homogeneity and purity of the material relative to the reference genome are characterized by comparing base calls from replicate datasets generated using multiple sequencing technologies. Genomic purity of the material is assessed by checking for DNA contaminants.
MutAid
Analyzes raw sequencing data from several next generation sequencing (NGS) platforms. MutAid is a pipeline performing six different steps: (i) quality control and filtering; (ii) mapping reads to reference genome; (iii) variant detection, effect prediction and cross-referencing and lastly (iv) and then produces a summary of all information generated. It can be used to interpret mutational variants from various data generated by targeted gene-panel sequencing or whole genome sequencing.
NGS-QCbox
A parallel, automated and rapid quality control pipeline for analyzing the next generation sequencing big data of Illumina platform. NGS-QCbox that scales up to process hundreds or thousands of samples. NGS-QCbox integrates Raspberry with other open-source tools for alignment (Bowtie2), SNP calling (SAMtools) and other utilities (bedtools) towards analyzing raw NGS data at higher efficiency and in high-throughput manner. It reports read and base statistics along with genome coverage and variants in a user friendly format. The pipeline developed presents a simple menu driven interface and can be used in either quick or complete mode. In addition, the pipeline in quick mode outperforms in speed against other similar existing QC pipeline/tools.
MO-FBA-FVA / MultiObjective-FBA-FVA
Provides two multi-objective extensions of constraint-based models (CBMs) for modeling communities: multi-objective flux balance analysis (MO-FBA) and multi-objective flux variability analysis (MO-FVA). Both MO-FBA-FVA pipeline methods were applied to a hot spring mat model ecosystem. As a result, multiple trade-offs between nutrients and growth rates, as well as thermodynamically favorable relative abundances at community level, were emphasized. This approach can be used for integrating genomic information in microbial ecosystems. These models will provide insights about behaviors (including diversity) that take place at the ecosystem scale.
BioVLAB / Biology Virtual Collaborative Labs
Provides a bioinformatics system for the integrated analysis of microRNA and messenger RNA (mRNA) data. BioVLAB is a cloud workbench that requires users to only perform two tasks: (1) create a virtual machine and then (2) download and execute a pre-composed workflow consisting of their own data. The software can be useful for small research labs that do not have access to high performance computing infrastructures and resources to hire full time bioinformatics and computer system specialists.
Mercury
Generates annotated personal genome suitable for further analysis and clinical interpretation. Mercury is an extensible workflow which comprises a library of multiple sequence analysis components including variant calling and annotation as well as a set of validation tools, with the aim of encompassing the complete field of the next generation sequencing (NGS) data analysis. Additionally, this software provides a cloud-based implementation to make information sharable between multiple users.
CIPHER
Automates the processing and analysis of several commonly used Next Generation Sequencing (NGS) datasets including: ChIP-seq, RNA-seq, Global Run On sequencing (GRO-seq), micrococcal nuclease footprint sequencing (MNase-seq), DNase hypersensitivity sequencing (DNase-seq), and transposase-accessible chromatin using sequencing ATAC-seq datasets. CIPHER provides an analysis mode that accomplishes complex bioinformatics tasks such as enhancer prediction. It supplies functions to integrate various NGS datasets together.
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