Displaying 1 to 9 from 9 results

ngless - NGLess: NGS with less work

Ngless is a domain-specific language for NGS (next-generation sequencing data) processing. Note: This is pre-release software, currently in beta (testing) It is stable enough to use, but there may still be some (minor) changes before an official release. For questions, you can also use the ngless mailing list.

jvarkit - Java utilities for Bioinformatics

Each tool is compiled independently of each other. See the documentation for each tool at http://lindenb.github.io/jvarkit/. All the pages should include a paragraph titled 'Download and Compile' You shouldn't try to compile all the tools because some of them are not tested, deprecated, or just too specific to my lab.

rvtests - Rare variant test software for next generation sequencing data

Rvtests, which stands for Rare Variant tests, is a flexible software package for genetic association analysis for sequence datasets. Since its inception, rvtests was developed as a comprehensive tool to support genetic association analysis and meta-analysis. It can analyze both unrelated individual and related (family-based) individuals for both quantitative and binary outcomes. It includes a variety of association tests (e.g. single variant score test, burden test, variable threshold test, SKAT test, fast linear mixed model score test). It takes VCF/BGEN/PLINK format as genotype input file and takes PLINK format phenotype file and covariate file. With new implementation of the BOLT-LMM/MINQUE algorithm as well as a series of software engineering optimizations, our software package is capable of analyzing datasets of up to 1,000,000 individuals in linear mixed models on a computer workstation, which makes our tool one of the very few options for analyzing large biobank scale datasets, such as UK Biobank. RVTESTS supports both single variant and gene-level tests. It also allows for highly effcient generation of covariance matrices between score statistics in RAREMETAL format, which can be used to support the next wave of meta-analysis that incorporates large biobank datasets.

Sarek - Detect germline or somatic variants from normal or tumour/normal whole-genome sequencing data

Previously known as the Cancer Analysis Workflow (CAW), Sarek is a workflow tool designed to run analyses on WGS data from regular samples or tumour / normal pairs, including relapse samples if required. It's built using Nextflow, a bioinformatics domain specific language for workflow building. Software dependencies are handled using Docker or Singularity - container technologies that provide excellent reproducibility and ease of use. Singularity has been designed specifically for high-performance computing environments. This means that although Sarek has been primarily designed for use with the Swedish UPPMAX HPC systems, it should be able to run on any system that supports these two tools.

minorseq - Minor Variant Calling and Phasing Tools

juliet identifies minor variants from aligned ccs reads. fuse reduces an alignment into its closest representative sequence.

iCallSV - A Framework to call Structural Variants from NGS based datasets

iCallSV is a Python library and command-line software toolkit to call structural aberrations from Next Generation DNA sequencing data. Behind the scenes it uses Delly2 to do structural variant calling. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina. We are in the process of publishing a manuscript describing iCallSV as part of the Structural Variant Detection framework. If you use this software in a publication, for now, please cite our website iCallSV.

NextGenMap - NextGenMap is a flexible highly sensitive short read mapping tool that handles much higher mismatch rates than comparable algorithms while still outperforming them in terms of runtime

NextGenMap is a flexible highly sensitive short read mapping tool that handles much higher mismatch rates than comparable algorithms while still outperforming them in terms of runtime. This allows analysing large scale datasets even with increased SNP rates or higher error rates (e.g. caused by specialized experimental protocols) and avoids biases caused by highly variable regions in the genome.

PHAT - Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform

The Pathogen-Host Analysis Tool (PHAT) is an application for processing and analyzing next-generation sequencing (NGS) data as it relates to relationships between pathogen and host organisms. PHAT provides quality control (QC) reporting on sequence files, alignment of sequence files against reference files, single-nucleotide polymorphism (SNP) prediction, linear and circular alignment viewing, and Excel and comma separated values (CSV) output. PHAT is under development in the Zehbe Lab (http://zehbelab.weebly.com/) at the Thunder Bay Regional Health Research Institute (TBRHRI) and Lakehead University (LU) under the supervison of Dr. Ingeborg Zehbe. This work is supported by a Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery grant to Dr. Ingeborg Zehbe (#RGPIN-2015-03855) and a NSERC Alexander Graham Bell Canada Graduate Scholarship-Doctoral (CGS-D) to Robert Jackson (#454402-2014).