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Showing 50 open source projects for "high"
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MongoDB Atlas runs apps anywhereMongoDB Atlas gives you the freedom to build and run modern applications anywhere—across AWS, Azure, and Google Cloud. With global availability in over 115 regions, Atlas lets you deploy close to your users, meet compliance needs, and scale with confidence across any geography.
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BBMap
BBMap short read aligner, and other bioinformatic tools.
...BBMap: Short read aligner for DNA and RNA-seq data. Capable of handling arbitrarily large genomes with millions of scaffolds. Handles Illumina, PacBio, 454, and other reads; very high sensitivity and tolerant of errors and numerous large indels. Very fast. BBNorm: Kmer-based error-correction and normalization tool. Dedupe: Simplifies assemblies by removing duplicate or contained subsequences that share a target percent identity. Reformat: Reformats reads between fasta/fastq/scarf/fasta+qual/sam, interleaved/paired, and ASCII-33/64, at over 500 MB/s. ... -
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NGSEP
NGSEP (Next Generation Sequencing Experience Platform)
NGSEP is an integrated framework for analysis of short and long DNA high throughput sequencing reads. The current version provides functionalities for both de-novo and reference guided analysis of sequencing data, including genome assembly, read mapping, variants detection and genotyping and de-novo analysis of data generated from reduced representation protocols. NGSEP also provides modules for analysis of genomic variation databases (VCF files), including functional annotation, filtering, format conversion, comparison, clustering, imputation, introgression analysis and different kinds of statistics. ... -
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sRNAWorkbench
The UEA sRNA Workbench
...Including expression profiling of known mirco RNA (miRNA), identification of novel miRNA in deep-sequencing data and identification of other interesting landmarks within high-throughput genetic data -
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PTESFinder
Post-Transcriptional Exon Shuffling (PTES) Identification Pipeline
...PTESFinder uses additional filters to exclude reads with ambiguous alignments around PTES exon-exon junctions, further increasing confidence in these supporting reads. PTESFinder identifies more PTES structures than other published methods whilst maintaining high specificity. -
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The Elvira project is a suite of tools to perform high-throughput genomic assemblies of repetitive, structured samples such as viruses or targeted regions of larger genomes.
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As of 2018-06-28, this project has moved to https://github.com/AdamaJava. This copy of the code will remain but all new code updates and releases will be from the new site. Java code developed by the Australian ICGC team for operating on next-generation sequencing data. This code is currently being maintained and expanded by the QIMR Berghofer Genome Informatics team (http://www.qimrberghofer.edu.au/lab/genome-informatics/) More details and documentation can be found on the...
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HIGH-THROUGHPUT TABULAR DATA PROCESSOR (HTDP) is Java application that is intended to facilitate data exploration and reduction tasks in large text files resulting from high throughput technologies, e.g. massively parallel sequencing or microarrays. The software has been optimized for microarray and deep parallel sequencing data, however it can accept any character delimited tabular data sets.
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DockoMatic is a GUI application that is intended to ease and automate the creation and management of AutoDock jobs for high throughput screening of ligand/receptor interactions.
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REHUNT
REHUNT (Restriction Enzymes HUNTing)
REHUNT (Restriction Enzymes HUNTing) is a free and open source package implemented in JAVA for providing many useful methods for biological sequence analysis (especially in SNP genotyping) around restriction enzymes. All academic researchers are encouraged to use REHUNT in their studies or to integrate it into their systems and applications. Non-academic users or commercial needs are also welcome to use it. For further information or additional applications, please contact the author... -
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Molecular Simulation Grid
Provides high performance computing power and state of the art tools
MoSGrid focuses on the configuration and provision of Grid services for molecular simulations and annotation of the results with metadata and their provision for data mining and knowledge generation. It is based on Liferay technology togethe with gUSE. -
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PriorityPruner is a software program which can prune a list of SNPs that are in high linkage disequilibrium (LD) with other SNPs in the list, while preferentially keeping SNPs of higher priority (e.g., the most significant SNPs in a genome-wide association study).
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Bamformatics
Toolkit and GUI for sequencing data analysis
The Bamformatics project aims to provide a coherent and consistent approach to analysis of high-throughput sequencing data. Its toolkit includes, among others, programs to identify variants and to compute various types genomic tracks. It also provides a graphical user interface to facilitate general bioinformatic workflows. The project wiki contains further details. -
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IAP.G2P
IAP - the Integrated Analysis Pipeline
The Integrated Analysis Platform (IAP) has been designed and developed to support the analysis of large-scale image data sets of different camera systems. It aims in bridging different data domains and in integrating different approaches to data analysis and post-processing. -
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Lab Storage
Rediscover the Simplicity http://www.atgclabs.com/
Help us to improve Freezer Web Access. We want to hear your feedback! Request new Freezer Web Access feature or module and receive a free Single User version with new feature. https://www.atgclabs.com/products/fw Freezer Web Access is a user friendly program designed to assist researchers with establishing an efficient system for storing frozen biological samples. FWA can track all of your research, development and process scale-up data in a single data storage platform, providing a... -
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Sample Tracking
Rediscover the Simplicity http://www.atgclabs.com/
Help us to improve Freezer Web Access. We want to hear your feedback! Request new Freezer Web Access feature or module and receive a free Single User version with new feature. https://www.atgclabs.com/products/fw Freezer Web Access is a user friendly program designed to assist researchers with establishing an efficient system for storing frozen biological samples. FWA can track all of your research, development and process scale-up data in a single data storage platform, providing a... -
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Hadoop-BAM is a Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework with the Picard SAM JDK, and command line tools similar to SAMtools. The file formats currently supported are BAM, SAM, FASTQ, FASTA, QSEQ, BCF, and VCF. For a longer high-level description of Hadoop-BAM, refer to the article "Hadoop-BAM: directly manipulating next generation sequencing data in the cloud" in Bioinformatics Volume 28 Issue 6 pp. 876-877, available online at: http://dx.doi.org/10.1093/bioinformatics/bts054 Note that the library part of Hadoop-BAM is mainly for developers with experience in using Hadoop. ...
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BioAnnote
Annotator Desktop application is able to annotate biomedical texts by
Annotator Desktop application is able to annotate biomedical texts by using different high-quality online resources, such as Medlineplus and Freebase. Users can introduce biomedical documents and obtain annotations for the relevant terms, such as diseases, symptoms and treatments. In addition, users can retrieve more detailed information for each recognized entity (making use of an integrated web browser), including related topics, external links, related bibliography and paper abstracts. -
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adLIMS
adLIMS: a Laboratory Information Management System with ADempiere
Many biological laboratories dealing with genomic samples are facing the problem of sample tracking, both for pure laboratory management and efficiency, and for internal policies, such as Good Laboratory Practices (GLP). Our laboratory exploits PCR techniques and next-generation sequencing (NGS) methods, to perform high-throughput integration site monitoring in different clinical trials and scientific projects, based on the delivery of therapeutic genes by viral vectors integrating into the genome of target cells. We process around 1500 samples/year resulting in hundreds of millions of sequencing reads, requiring automation and posing new challenges in data storage, monitoring of sample process and computational tools for analyses. ... -
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picard
A set of tools for working with high-throughput sequencing data
A set of tools (in Java) for working with next generation sequencing data in the SAM/BAM format. Note that development has moved to GitHub at https://github.com/broadinstitute/picard and support is available on the GATK forum at http://gatkforums.broadinstitute.org/categories/ask-the-team -
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GenoCAD is a CAD software for synthetic biology. This application provides a web-based tool to design plasmids, artificial gene networks, and other synthetic genetic systems composed of standard genetic parts. It includes a parts management system, a rule-based design tool, and a simulation engine. This project has morphed into a SaaS model. The open source code is no longer maintained.
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vipR is a program to screen for sequence variants (SNPs, deletions) in sequence data generated by high-throughput-sequencing platforms. Information on this and other projects can be found on: http://www.altmann.eu
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This library aims to provide support for D-dimensional images in Java and to enable high-level implementation of algorithms in dimensionally-invariant manner. Major features: the dimensionality and the access to primitive data types are abstracted.
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TriageTools
Tools for partitioning and prioritizing fastq data
TriageTools is a collection of tools for partitioning raw data (fastq reads) from high-throughput sequencing projects. The tools are designed for basic data management as well for prioritizing analysis of certain subsets. The project wiki contains usage information. -
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cmotif
A method for mining conditional phosphorylation motifs
...Although several algorithms have been proposed to uncover phosphorylation motifs, the problem of efficiently discovering a set of significant motifs with sufficiently high coverage and non-redundancy still remains unsolved. In this paper, we propose an algorithm called C-Motif for a non-redundant identification of significant phosphorylation motifs. In tests with real data including both non-kinase-specific and kinase-specific phosphorylation data, the C-Motif algorithm successfully reports a relatively complete set of of conditional phosphorylation motifs efficiently. -
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The goal of this project is to combine different sources of information as well as methods to help in the process of gap closing / genome finishing in high throughput sequencing.
