Search Results for "vcf"
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Showing 16 open source projects for "vcf"
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NGSEP
NGSEP (Next Generation Sequencing Experience Platform)
...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. Since version 4, we provide functionalities for management of genomes and transcriptomes, including genome alignment and annotation of transposable elements. A complete list of functionalities is available in our wiki (https://sourceforge.net/p/ngsep/wiki/Home/). ... -
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123VCF
An Intuitive and Efficient Tool for VCF file filtration
123VCF has been developed to make the filtration step of VCF files efficient and more importantly easy to understand. It can be used in the most important step of whole exome/genome sequencing data analysis in the research and also clinical settings. User manual: https://dl.adbioinformatics.net/123VCF/123VCF_Manual.ver2.pdf If you use 123VCF, please cite its paper: Eidi, M., Abdolalizadeh, S., Moeini, S. et al. 123VCF: an intuitive and efficient tool for filtering VCF files. ... -
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GnuAccounting
Cross-plattform java invoicing and accounting application
An open-source java accounting application that integrates OpenOffice, Apache Derby and HBCI/FinTS to create and manage invoices, credit memos, delivery notes, bills etc. Imports from kTimeTracker, Task Coach, VCF, Hibiscus, Moneyplex, Starmoney, exports to Winston, VCF, openTrans et. al. -
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...The software has been optimized for microarray and deep parallel sequencing data, however it can accept any character delimited tabular data sets. HTDP can also import, process and convert Variant Call Format (VCF) files ver. 4.0, 4.1 and 4.2 (http://samtools.github.io/hts-specs/VCFv4.2.pdf). HTDP provides quick filtering functionality and can process data consisting of single or multiple input files. Citation: Madanecki P, Bałut M, Buckley PG, Ochocka JR, Bartoszewski R, Crossman DK, et al. (2018) High-Throughput Tabular Data Processor – Platform independent graphical tool for processing large data sets. ...
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VCF Split
Vcard File Splitter
This little Java Program splits a VCF file consisting of multiple vcarss into single files. This is particualry useful if you want to import a vcf into Microsoft Outlook. It ist a executable jar file, so starting it with java -jar vcfsplitter.jar or double clicking it in a gui should work fine. You can also specify evertyhing by command line as follows: java -jar vcfsplitter.jar <infile> <outdir> For the source click on the website link.. -
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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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Auto Primer3
Automatically design primers to genes/coordinates using primer3.
PLEASE NOTE: THIS PROJECT PAGE WILL NO LONGER BE UPDATED - PLEASE USE THE GITHUB PAGE (https://github.com/gantzgraf/autoprimer3) TO FIND THE LATEST RELEASE (https://github.com/gantzgraf/autoprimer3/releases/latest). AutoPrimer3 retrieves gene information, DNA sequences and SNP information from the UCSC genome browser and uses primer3 to automatically design primers to genes or genomic coordinate targets. Primers may be designed using information from any of the UCSC hosted genomes... -
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HomSI
Homozygous Stretch Identifier from next-generation sequencing data
...Recently, the advent of next generation sequencing enables the concurrent identification of homozygous regions and the detection of mutations relevant for diagnosis, using data from a single sequencing experiment. In this respect, we have developed a novel tool that identifies homozygous regions using deep sequence data. Using *.vcf files as an input file, our program identifies the majo -
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Athus
Manage, merge, filter and convert population genetics data
This project assists you in performing population genetic analyses by taking over the ugly, boring and error-prone data manipulation steps. Starting from well specified input formats VCF, BED and FASTA and a unique configuration file describing data (f.e. from SNP-arrays or sequencing) as well as filtering one can create standard POPGEN formats like Eigenstrat, PEDMAP (PLINK), Treemix ... In addition there are several utilities for * generating VCF from SNPArray data (NCBI - GEO, Illumina call files) * work with genetic maps ... -
Error to trace to log to deploy. One click. No SSH.AppSignal links every error to the trace, the trace to the log, the log to the deploy that shipped it.
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Andoffline
A toolkit for some Android sms/call Apps, base64 encoder, vcf parser a
MOVED TO: https://github.com/fulvio999/Andoffline Feature: Browser for exported SMS, CALL and CONTACT from Android Phone Save to PDF file for exported SMS, CALL and CONTACT, VCF parser Support tool for: http://android.riteshsahu.com/apps/sms-backup-restore http://android.riteshsahu.com/apps/call-logs-backup-restore Image base64 encoder/decoder ** Allow to execute job/script execution from SMS sent from remote phone (without internet connection): - connect the phone to PC with usb - Install the Android App - create a job on desktop application - start PC listener and Phone receiver ** See pdf guide for more details - web application to manage job/script stored in a relational DB (Mysql or sqlite). ... -
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QR Gen
Multi-platform QR code generator from information supplied
QRGen creates QR codes from contact information, written in Java. It requires the tool qrencode in order to work, qrencode is freely available at http://fukuchi.org/works/qrencode (Linux/Mac OS/UNIX) , or http://code.google.com/p/qrencode-win32/ (Windows), or Ubuntu Software Centre. -
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PhonixJ
A cross-platform phone-book written in Java using SWT.
...Features: - Add/remove contacts - Create vCard v.3.0 - Create Contact Card in .SVG - Create mail envelope address - Sophisticated search engine - Customizable printing options - Support for email and browser clients - Batch export/import of the contacts via .vcf (3.0) files (tested with Kontact) - A tool to select multiple e-mail addresses, copy them to clipboard and open compose mail Current version: 1.0.3 News: - Added notes record to each contact - If you want to see it in your own language, please download the Main.properties, and translate it, then send it back to me. Please contact me if you'd help, and specify your special needs if any. -
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This is a simple program that allows you to get the information in a vCard file (.vcf) as plain text. vCards are used to store contact information and may be created by Apple's Address Book and other similar programs, along with mobile phones.
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"Wiki in a Jar" is a small Wiki written in Java with great focus on simplicity. It is intended to run on a USB stick as a replacement for a paper note- and address book as a Personal Information Manager (PIM). It supports vcard (vcf) contact files.
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SynthLab is a sound synthesis witch provide several modules you can plug to each over via a graphical interface such as a VCO, a VCF, a VCA, an envelop, ... You can use a direct sound output or save to a file
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