Search Results for "throughput" - Page 11
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Showing 350 open source projects for "throughput"
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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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iCAS - An Illumina Clone Assembly System
An Illumina clone assembly system using SOAPdenovo and ABySS
Clone-by-clone sequencing, as a means of achieving high quality assemblies for large and complex genomes, continues to be of great relevance in the era of high throughput sequencing. However, assemblies obtained using current whole genome assemblers are often fragmented and sometimes have issues of genome completeness owing to different data characteristics introduced by multiplexed sequencing. With iCAS the data filtering process is based on a novel kmer frequency algorithm, resulting in near perfect pre-assembly reads. ... -
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ncmock
NetCDF mock data generator.
...Global and variable attributes can also be created. Esoteric controls exist for choosing alignment, blocksize, file flavor (classic or HDF5), prefill, initial size, and header pad. ncmock has throughput and peak memory calipers, so it can also be used as a benchmark tool -
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HTSeq
Analysing high-throughput sequencing data with Python
This SourceForge page is outdated! HTSeq has been moved to github: https://github.com/simon-anders/htseq General information and documentation on HTSeq; http://www-huber.embl.de/users/anders/HTSeq -
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EDDA
Experiment Design for Differential Abundance Analysis
...EDDA can aid in the design of a range of common experiments such as RNA-seq, ChIP-seq, Nanostring assays, RIP-seq and Metagenomic sequencing, and enables researchers to comprehensively investigate the impact of experimental decisions on the ability to detect differential abundance. More details of EDDA can be found at Luo, Huaien et al. “The Importance of Study Design for Detecting Differentially Abundant Features in High-Throughput Experiments.” Genome Biology 2014;15(12):527 (http://www.ncbi.nlm.nih.gov/pubmed/25517037/). An accompanying web server (http://edda.gis.a-star.edu.sg/) is available for easy access to some functionality of EDDA. Additionally a Bioconductor package (http://www.bioconductor.org/packages/release/bioc/html/EDDA.html) is available for easy installation of EDDA R package. -
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Plant Senescence Analysis
Accurate analysis of plant senescence by colour distortion corr
...However, manual inspection is time consuming and its evaluation is subjective. Therefore objective valuation of plant senescence by color image analysis is desirable for high throughput plant phenotyping. The plant colors in images may not represent the original colors of plants due to imperfect camera lenses and camera settings. In this case, color analysis for the senescence estimation may result in significant error. In this method, we propose a novel algorithm to have the effects of both the color distortion correction and the deblurring for senescence analysis. -
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Telomerecat: The Telomere Computatioanl Analysis Tool Telomerecat allows you to generate average TL estimates for any high throughput paired end sequencing samples.
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SALAM
Statistical Analysis of Larval Motions
Automated, high-throughput detection and statistical analysis of behaviors of Drosophila larvae. -
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WebPing
Track the *REAL* Performance of your Web Site
Project Web Ping - If you use an ISP for your web-hosting, you will discover that your 'ping' requests have been re-directed. By timing the response from an actual web-hosted URL, Web Ping allows us to document the *REAL* throughput to our Web Sites. Data collected are down-loadable in a CSV Format. (See ClassIO or your favourite spreadsheet-program for an easy way to re-use these data.) -
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Flexbar
flexible barcode and adapter removal for sequencing platforms
Flexbar moved to https://github.com/seqan/flexbar The program Flexbar processes high-throughput sequencing data efficiently. It demultiplexes barcoded runs and removes adapter sequences. Moreover, trimming and filtering features are provided. Flexbar supports next-generation sequencing data in fasta and fastq format, e.g. from the Illumina platform. Reference: Matthias Dodt, Johannes T. Roehr, Rina Ahmed, Christoph Dieterich: Flexbar — flexible barcode and adapter processing for next-generation sequencing platforms. ... -
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JAABA
The Janelia Automated Animal Behavior Annotator
...JAABA uses machine learning techniques to convert these manual labels into behavior detectors that can then be used to automatically classify the behaviors of animals in large data sets with high throughput. JAABA combines an intuitive graphical user interface, a fast and powerful machine learning algorithm, and visualizations of the classifier into an interactive, usable system for creating automatic behavior detectors. Documentation is available at: http://jaaba.sourceforge.net/ -
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Apache Kafka
Mirror of Apache Kafka
Apache Kafka is a distributed streaming platform built around durable, partitioned logs called topics, enabling high-throughput, fault-tolerant event pipelines. Producers append records to partitions, brokers replicate them for durability, and consumer groups read them at their own pace while balancing work across instances. The commit/offset model and retention policies support patterns from real-time processing to event sourcing and audit trails. Exactly-once processing semantics, idempotent producers, and transactions help prevent duplicates across complex dataflows. ... -
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GUItars
GUItars is designed for the analysis of high throughput RNAi data.
Please refer to the original article published in PLOS ONE at http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0049386. GUItars's user-friendly graphical interface enables rapid analysis of RNAi and small molecule screens. GUItars uses SSMD for hit selection, which is preferred for its ability to diminish sample size effects and the false hit rate, making it superior to other widely used HTS analysis methods. The program can handle the analysis for screens without... -
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AmpEx
AmpEx Amplicon Extractor
AmpEx is a tool that aims to extract in silico amplicons from high-throughput data. In particular, AmpEx is able to detect amplicons flanked by primer pairs with homopolymer expansions from 454 pyro-reads. -
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MRelay
Host to Host Network Acceleration and Encryption
MRelay splits and distributes the traffic of a single TCP connection to several connections and merges the data at the other end. Using this approach, it is possible to achieve high throughput between two points on the network regardless of the delay between two points. MRelay can optionally encrypt the data and exchange some http headers before the relay process to make the traffic look like a regular http file download. This can be used to overcome the highly restrictive firewalls that are content-sensitive or can detect and block VPN traffic. ... -
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GenomicVis
Genomic data visualisation
GenomicVis is a R package that contains a collection of function for the visualisation of genomic data typically derived from high-throughput whole genome sequencing and SNP-Chip experiments. Most of the functions provided by this package are agnostic about where the data actually comes from, that is, they required input in simple data.frame instances that are not tied to a particular file format; however, we also provide many examples of creating these simply data.frames from standard file formats such as VCFs and from common software tools such as GAP and Breakdancer -
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iMS2Flux is a command line based high-throughput processing tool set for stable isotope labelled mass spectral data targeting metabolic flux analysis. To get started simply download and unzip the iMS2Flux.zip file and follow the getting started document for your OS. Current version 7.2.1 (last updated 9/30/2014) - Completes support and correction functionality for a new user specified generic data class.
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Network Analyzer
Analyze the network carateristics like Delay, Jitter, Packet loss etc.
...(The receiving host is then required to echo all the packets back to the sender, which can be easily done via iptables rule under linux). Once the eched packets arrives back to the sender, the analyzer will calculate all the related statistics like, packet loss, jitter throughput etc... NOTE: in order to receive the echo packets you must configure the receiving host to echo the incoming packets. In the next release i will provide another java application that just echo on an UDP port. -
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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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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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DNA metabarcoding, which takes advantage of high throughput capacity of next-generation-sequencing (NGS) platforms, has emerged for characterizing the biodiversity of large volumes of eukaryote samples that consist of upwards of hundreds of thousands of individuals and thousands of species.
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Mutascope
Analysis software designed for PCR-amplicon sequencing data.
Mutascope is a software suite designed to analyze data from high throughput sequencing of PCR amplicons, with an emphasis on normal-tumor comparison for the accurate and sensitive identification of low prevalence mutations. -
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RDP FrameBot is a frameshift correction and nearest neighbor classification tool for use with high-throughput amplicon sequencing. It uses a dynamic programming algorithm to align each query DNA sequence against a set of target protein sequences, produces frameshift-corrected protein and DNA sequences and an optimal global or local protein alignment. It also helps filter out non-target reads. The online version of FrameBot is available on http://fungene.cme.msu.edu/FunGenePipeline, tutorial http://rdp.cme.msu.edu/tutorials/framebot/RDPtutorial_FRAMEBOT.html. ...
