Search Results for "sam tool"
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Showing 25 open source projects for "sam tool"
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AWS SAM CLI
CLI tool to build, test, debug, and deploy Serverless applications
The AWS Serverless Application Model (SAM) CLI is an open-source CLI tool that helps you develop serverless applications containing Lambda functions, Step Functions, API Gateway, EventBridge, SQS, SNS and more. The AWS Serverless Application Model (SAM) is an open-source framework for building serverless applications. It provides shorthand syntax to express functions, APIs, databases, and event source mappings. -
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SAM is a command line tool (for Slackware Linux) which uses a stack to provide control of variables, including PATH, and functions. To do this it uses a set of scripts, functions and compiled code. The result is a command line environment that changes the way you see and thus changes the way you think. It has helped me to write more and better shell code.
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SIREN
Renewable Energy Network tool
SIREN demonstrates how electricity demand may be met by a mix of renewable energy sources. Users explore potential location and scale of renewable energy sources (stations, storage, transmission) to meet electricity demand. SIREN allows you to build scenarios for the energy mix for your area of interest. It is based around the map of your chosen area and allows you to visualise the layout of the existing electricity network plus the additional stations you place on the map to build your... -
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BBMap
BBMap short read aligner, and other bioinformatic tools.
...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. BBDuk: Filters, trims, or masks reads with kmer matches to an artifact/contaminant file. ...and more! -
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123FASTQ
An intuitive and efficient tool for preprocessing Illumina FASTQ reads
123FASTQ performs all the pre-processes of Illumina next-generation sequencing reads (FASTQ files) easier than ever. Download the quick user manual for the latest version: https://dl.adbioinformatics.net/NGSNeeds/myTools/123Fastq_v1.3_Manual.pdf Authors: Milad Eidi, Samaneh Abdolalizadeh, Mohammad Hossein Nassirpour Supervisors: Javad Zahiri, PhD University of California San Diego Masoud Garshasbi, PhD Tarbiat Modares University, Tehran, Iran If you use 123FASTQ,... -
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ASLoader
Arduino upload tool
This little Java tool allows you to upload a compiled sketch to your Arduino without using the IDE. Currently the protocols Stk500v1, Stk500v2, Avr109 and SAM-BA are implemented. That means the * Arduino Due, * Arduino Duemilanove, * Arduino Leonardo, * Arduino Leonardo ETH, * Arduino Mega, * Arduino Micro, * Arduino Nano, * Arduino Pro Mini, * Arduino Uno and maybe some others are supported. -
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miRDeep*
MiRDeep*
Please cite: An, J., Lai, J., Lehman, M.L. and Nelson, C.C. (2013) miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data. Nucleic Acids Res, 41, 727-737. We will create index for you if you tell us your interested species (j.an@qut.edu.au). download command line version "MDS_command_line_Vxx.zip" clicking "Browse All Files" please find miRPlant in sourceforge for plant miRNA prediction. -
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FastQC
A quality control analysis tool for high throughput sequencing data
FastQC is a quality control analysis tool designed to spot potential problems in high throughput sequencing datasets. Its goal is to provide a simple way by which to check the quality of raw sequence data coming from high throughput sequencing pipelines. It does this by running a modular set of analyses on one or more raw sequence files in fastq or bam format. It then produces a report summarizing the results, and highlighting any areas where the library may appear unusual. This should then... -
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PDFsam Portable
Split, merge, extract pages, mix and rotate PDF files.
...It has all the same features as PDFsam Basic, plus, it leaves no personal information behind on the machine you run it on, so you can take it with you wherever you go. The ‘sam’ part of PDFsam's name means ‘split and merge’, and this is a large part of what the tool is designed to do. As well as making it possible to merge multiple PDFs into a single file, PDFsam Basic offers you no fewer than three ways to split PDFs. You can split using page numbers as a marker, using bookmarks contained within a PDF file, or into chunks of a particular size. ... -
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miARma-Seq
a A suite designed to study mRNAs, miRNAs and circRNAs
miARma-Seq, which stands for miRNA-Seq And RNA-Seq Multiprocess Analysis, is a suite designed to study mRNAs, miRNAs and circRNAs. It is able to perform differential expression analysis, miRNA-mRNA target prediction and functional analysis among others. Most importantly, it can be applied to any sequenced organism, and it can be initiated at any step of the workflow. As a stand-alone tool, is both easy to install and extremely flexible in terms of its use. It brings together... -
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MITP
MITP - conserve & novel miRNA identification & target prediction tool
miRNA is a widely known small non-coding RNA which can mediate gene regulation of most important biological processes in plants and animals. Therefore, identification conserve and novel miRNA and their target genes in model and new sequenced species are inevitable. MITP is designed to identify miRNA easily and faster based on sequence mapping result from any mapping software which producing SAM format output result, blast result (default output result) or blat result (default output result).... -
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CoverageAnalyzer
RNA modification detection by RT signatures in deep sequencing data
...Consequently, the community will profit from a platform seamlessly connecting detailed visual inspection of RT signatures and automated screening for modification candidates. CoverageAnalyzer was developed in response to the demand for a powerful inspection tool, running on all 3 OSes. With SAM standard as input and an intuitive GUI, even non-experts can accomplish a variety of tasks, from visualization of RNA Seq data, up to sophisticated modification analysis with significance-based candidate calling. -
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sameflash
Serial flash tool for Atmel M7 core
This tool written in Java uploads HEX files into microcontroller flash and runs it using SAM-BA protocol, as original Atmel tool fails with modern M7 core chips. SAME70 is now supported. Current version does not program GPNVM bit, so after reset program will not start again - just add few lines of code to do that. -
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samdrives
Monitor and control multiple SAM/QFS servers
samdrives is a tool for monitoring and controlling tape drives on multiple SAM/QFS servers simultaneously. It monitors performance (same as iostat), drive status (same as "samu t"), and allows controlling archiving, staging and tape drives remotely. -
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SAMSVM
A tool for misalignment filtration on SAM-format sequences with SVM
Applying the LIBSVM, a package of support vector machine, SAMSVM was developed to correctly detect and filter the misaligned reads of SAM format. Such filtration can reduce false positives in alignment and the following variant analysis. -
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LDS
LDS (Loop Diagnostic System) an Electronic Agen
LDS (Loop Diagnostic System) is an Electronic Agent written in VB Net including over 30 Applications in telecommunication field as: Line Test Diagnostic Application, Batch Diagnostic Tools, NGN Script Generator Tool, SS7 Trace Analysis Tool (MeGaCo, IAM, SAM, COT, CPG, SUS, UDT, ACM, ANM, REL, OPM, H248, RTP Trace Analysis), RDP (Remote Desktop) Client Application, GIS Tool, xDSL Tools & Loop Calculator Application, Auto Response Generator Tool, OS Emulators Tool, Router GUI Emulators Tool, ISP Services Tool, TMS (Troubleshooting Management System) Application, Unit Converter Tool, CLI Reverse Lookup Tool, Phonebook Tool, NT1 Commands Tool, Dynamic Guide Application etc -
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MethylExtract
High-Quality methylation maps and SNV calling from BS-Seq experiments
MethylExtract is a user friendly tool to generate i) high quality, whole genome methylation maps and ii) to detect sequence variation within the same sample preparation. The program is implemented into a single script and takes into account all major error sources: sequencing errors, bisulfite failure, clonal reads and single nucleotide variants. MethylExtract detects variation (SNVs – Single Nucleotide Variation) in a similar way than VarScan, a very sensitive method extensively used in... -
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unixadmin
unixadmin is a system administration tool for Linux and OS X
unixadmin ============ unixadmin (Previously known as smc/syspert) Is a system administration tool which supports all versions of UNIX and Debian based versions and Red Hat versions of Linux, which supports major features such as user administration, disk administration and system administration This program sets to replace smit in IBM AIX and sam in HP-UX This program is the Linux equivlient of smit and SAM in AIX and HP-UX -
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Configuration Grabber
configgrab
The configuration grabber (configgrab for short) fetches a list of devices and retreives the configuration from them. The tool is targeted towards routers and other remote devices that do not contain powerful utilities like rsync. -
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Multi-Pipeline Gene Expression Analysis
Helps users to determine the optimal gene expression analysis pipeline
The Multi-Pipeline Gene Expression Analysis tool was developed as a prototype during the Bioinformatics Integration Support Contract (BISC) in 2010-2011. It was available online at the ImmPort website in an "Alpha" release until November 2013. The tool utilizes about 300 gene expression analysis pipelines with combinations of methods for: 1. Background Correction (none, mas5, rma, DFCM, RMA-mean, RMA-75) 2. -
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SAMMate
RNA-Seq Transcriptome Assembly and Analysis
SAMMate is a GUI software tool for processing SAM files. The software allows users to accurately estimate gene expression and isoform expression scores using short reads to generate wiggle files for visualization in UCSC genome browser and an alignment statistics report. -
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GodFather Five Families Tool
GodFather Five Families Tool
Discontinued "Hi, We noticed that you have created a program that takes players coordinates and places them into a 3rd party program that is then searchable by other players. After consulting with out legal team, I was informed that this is actually a violation of our Terms of Service. We respectfully ask that you remove the program from download. Thank you for your cooperation in the matter, -Sam" -
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BSD SAM-BA is a free tool under ISC licence. Like the xp SAM Boot Assistant (SAM-BA.exe) this software provides a means of easily programming different AT91 devices. Communicating with the target device may be done through an RS232 or a USB link.
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