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NextFlow
Enables pipeline development through the adaptation of existing pipelines written in any scripting language. NextFlow is a workflow management system using Docker technology for the multi-scale handling of containerized computation. The software is designed to address numerical instability, efficient parallel execution, error tolerance, execution provenance and traceability. Users can run any current or previous version of a pipeline for any published and properly deposited analyses.
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.
SeqMule
A computational pipeline to perform automated variant calling from NGS data on human genomes and exomes. SeqMule integrates computational-cluster-free parallelization capability built on top of the variant callers, and facilitates normalization/intersection of variant calls to generate consensus set with high confidence. SeqMule integrates 5 alignment tools, 5 variant calling algorithms and accepts various combinations all by one-line command, therefore allowing highly flexible yet fully automated variant calling.
OpEx / Optimised Exome
Comprises a fixed implementation of alignment, calling and annotation tools optimised for individual/multiple exome sequencing analysis in the clinical setting or the research. OpEx is customizable with options available in its configuration file, this including setting the reference genome manually and changing the transcript database. This tool uses Platypus for variant calling, which provides equivalent performance irrespective of the number of exomes being analysed.
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.
IMPACT / Integrating Molecular Profiles with ACtionable Therapeutics
A whole exome sequencing (WES) data analysis pipeline that integrates both single nucleotide variants and copy number alterations from WES data to identify a list of candidate genes for therapeutic targets. IMPACT returns a prioritized list of drugs predicted to target these cancer genes using a drug-target database. IMPACT analysis pipeline also allows users to explore the tumor heterogeneity of the sample. This allows users to understand the clonal dynamics from WES data during the course of treatments, or comparisons of clinically similar samples to each other.
Fastq2vcf
An integrated analysis pipeline for whole-exome sequencing (WES) data analysis. Fastq2vcf offers improved flexibility, efficiency, and reproducibility. It can generate shell scripts that automate the steps for processing WES data from raw sequence reads to annotated variants. It is also highly configurable and provides users with complete control of the processing procedure, making it easy to submit and track jobs in both single workstation and parallelized computing environments.
SeqBench
Supports the management and analysis of exome sequencing data. SeqBench combines data management, data analysis, and result visualization into a single web-based platform. The software is a web-based application that embeds the analysis pipeline SIMPLEX and provides a data acquisition module supporting data derived from Illumina and SOLiD platforms. The server provides a user interface, facilitates comprehensive data acquisition through a wizard system and can be installed as an out of the box solution.
EthSEQ
An R script that allows to infer ethnicity of a set of samples for which whole exome sequencing (WES) data is available from differential SNP genotypes profiles. EthSEQ combines the 1,000 Genomes Project genotype data, used to generate reference models for specific WES platforms; the ASEQ, used to genotype the input samples with unknow ethnicity; and the EIGENSTRAT, used to perform principal component analysis on the aggregated genotyped data. This tool can be integrated into any WES based processing pipeline and exploits multi-core capabilities.
bcbio-nextgen
A python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis. You write a high level configuration file specifying your inputs and analysis parameters. This input drives a parallel pipeline that handles distributed execution, idempotent processing restarts and safe transactional steps. The goal is to provide a shared community resource that handles the data processing component of sequencing analysis, providing researchers with more time to focus on the downstream biology.
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