Search Results for "sam"
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Showing 24 open source projects for "sam"
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Bowtie 2
A fast and sensitive gapped read aligner
...It is especially effective for reads ranging from around 50 bases to hundreds or thousands of characters, and it supports modern sequencing workflows that require gapped, local, and paired-end alignment. The tool builds compact FM-index-based reference indexes, keeping memory usage low even for large genomes like the human genome. Bowtie 2 outputs alignments in SAM format and includes companion utilities for building and inspecting indexes. It is widely used in bioinformatics pipelines for RNA-seq, DNA-seq, metagenomics, variant analysis, and other sequencing-based research tasks. Overall, Bowtie 2 remains a foundational command-line tool for high-throughput sequence alignment and reproducible computational biology workflows. -
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i2pd
I2P: End-to-End encrypted and anonymous Internet
i2pd (I2P Daemon) is a lightweight, full-featured C++ implementation of the I2P (Invisible Internet Project) protocol, designed for enabling anonymous, encrypted, and censorship-resistant communication. It functions as a router node in the I2P network, supporting services like anonymous websites (eepsites), email, file sharing, and secure messaging. i2pd is designed to be resource-efficient and suitable for running on embedded systems or routers while maintaining compatibility with the wider... -
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RECOIL
Retro Computer Image Library
Retro Computer Image Library decodes Amiga, Amstrad CPC, Apple II, Atari 8-bit, Atari Portfolio, Atari ST/TT/Falcon, BBC Micro, Commodore 64, Commodore 16/116/Plus4, Commodore 128, Electronika BK, FM Towns, HP 48, Macintosh 128K, MSX, NEC PC-80/88/98, Oric, SAM Coupe, Sharp X68000, Tandy 1000, Timex 2048, TRS-80, TRS-80 Color Computer, ZX81 and ZX Spectrum picture formats. The project contains a simple viewer, plug-ins for general-purpose image viewers and editors, and an everything-to-png converter. -
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GapFiller
A de novo local assembler for paired reads
GapFiller is a seed-and-extend local assembler to fill the gap within paired reads. It can be used for both DNA and RNA and it has been tested on Illumina data. GapFiller can be used whenever a sequence is to be assembled starting from reads lying on its ends, provided a loose estimate of sequence length. -
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ophcrack
A Windows password cracker based on rainbow tables
Ophcrack is a Windows password cracker based on a time-memory trade-off using rainbow tables. This is a new variant of Hellman's original trade-off, with better performance. It recovers 99.9% of alphanumeric passwords in seconds. -
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ScummVM
A cross-platform interpreter for many point-and-click adventure games
ScummVM is a cross-platform interpreter for many point-and-click adventure games. This includes LucasArts SCUMM games (such as Monkey Island 1-3, Day of the Tentacle, Sam & Max, ...), many of Sierra's AGI and SCI games (such as King's Quest 1-6, Space Quest 1-5, ...), Discworld 1 and 2, Simon the Sorcerer 1 and 2, Beneath A Steel Sky, Lure of the Temptress, Broken Sword 1 and 2, Flight of the Amazon Queen, Gobliiins 1-3, The Legend of Kyrandia 1-3, many of Humongous Entertainment's children's SCUMM games (including Freddi Fish and Putt Putt games) and many more. ... -
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sfbf-ui
UI frontend for sfbf, a useful application to search for largest files
UI frontend for sfbf, a useful application to search for largest files on file systems It brings features such as : - Fast file search to locate largest files - Configurable search depth - Various export formats (txt, json, xml, html) - Regular expression matching This project is licensed under the WTFPL (Do What The Fuck You Want To Public License, Version 2) Copyright © 2017 spypunk spypunk@gmail.com This work is free. You can redistribute it and/or modify it under the terms of the Do What The Fuck You Want To Public License, Version 2, as published by Sam Hocevar. See the COPYING file for more details. -
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sfbf
Useful console application to search for largest files on file systems
...It brings features such as : - Fast file search to locate largest files - Configurable search depth - Various output formats (txt, json, xml, html, csv) - Regular expression matching This project is licensed under the WTFPL (Do What The Fuck You Want To Public License, Version 2) Copyright © 2017 spypunk spypunk@gmail.com This work is free. You can redistribute it and/or modify it under the terms of the Do What The Fuck You Want To Public License, Version 2, as published by Sam Hocevar. See the COPYING file for more details. -
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Barracuda is a high-speed sequence aligner based on Sanger's BWA and utilizes the latest Nvidia CUDA architecture for accelerating alignments of sequence reads generated by next-generation sequencers.
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A fork of BOSSA
This is a fork of the BOSSA project by ShumaTech.
BOSSA is a flash programming utility for Atmel's SAM family of flash-based ARM microcontrollers, developed by ShumaTech. The motivation behind BOSSA is to create a simple, easy-to-use, open source utility to replace Atmel's SAM-BA software. This project is a fork, created to temporarily host new modifications to BOSSA until they can be incorporated into the main BOSSA codebase. -
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Simple Automation Middleware (SAM) est un framework permettant de batir des applications sous forme de modules. Il fournit des bibliothèques COM Delphi implémentant la gestion des évènements, Dispatch etc...
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bio-cargo
CARGO - Compressed ARchival for GenOmics
CARGO is a high-level framework that can semi-automatically generate software systems optimized for the compressed storage of arbitrary types of large genomic data collections. Straightforward applications of CARGO methods to compress FASTQ and SAM format archives require only a few lines of code, produce solutions that match and sometimes outperform specialized format-tailored compressors, and scale well to multi-TB datasets. -
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sam_comp
Compression for SAM/BAM file format
This is a simple arithmetic coding based compressor for the SAM and BAM (DNA sequence alignment) file format. -
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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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MIF85Tracker
chiptune music tracker for Philips SAA-1099
Multiplatform GNU/GPL chiptune music tracker for Philips SAA-1099 soundchip with 6 channels, which was used in Sam Coupé micro-computer and also in sound interface MIF 85 for the Tesla PMD 85 (an 8-bit personal micro-computer produced in eighties of twentieth century in former Czechoslovakia). This is a very first music tracker for this soundchip on PC platform! -
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Object-oriented Simple DirectMedia Layer
High-level C++ framework to ease game development
OSDL: Object-oriented Simple DirectMedia Layer. OSDL is a high level open source (LGPL/GPL) portable multimedia library, built upon Sam Lantinga's SDL (http://www.libsdl.org). Its goal is to provide a high level C++ framework to ease game development. -
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This has now moved to GitHub! https://github.com/sam-truscott/wumpusopenal Output Plug-in for Winamp 5 that utilises OpenAL. Written primarily for Windows Vista and Windows 7 users to get Hardware Acceleration support.
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HPeak
A HMM-based algorithm for defining enriched regions from ChIP-seq data
...Command (single-end): perl /compbio/software/HPeak3/HPeak.pl -sp HUMAN/MOUSE -format BED -t TREATMENT.inp -c CONTROL.inp -n OUTPUTPREFIX -fmin 100 -fmax 300 -r 36 -ann -wig -seq -interfiles Command (pair-end): perl /compbio/software/HPeak3/HPeak.pl -sp HUMAN/MOUSE -format BED -pe TREATMENT.inp -c CONTROL.inp -n OUTPUTPREFIX -isize 200 -r 100 -pec (if control is PE) -ann -wig -seq –interfiles note: 1. Default species is HUMAN. Also supports MOUSE. Can add any other genome if in need. 2. Default format is BED. Also support ELAND. Will add SAM and BAM. 3. –r specifies read length (this is import through my experience). 4. –pe indicates pair-ended data. 5. If data is pair-ended, -isize refers to insert size (total length of a pair). -
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samscope
A lightweight OpenGL SAM/BAM viewer
A lightweight OpenGL based interactive SAM/BAM viewer. Quickly and easily generate aggregate statistics from SAM/BAM files like coverage, polarity, and minor allele frequencies, then scroll and explore freely with a simple mouse based interface. Multiple windows can be synchronized for careful comparison across multiple experiments. -
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T-REX and Muscle SAM big trouble in SPF
A graphic adventure in the wrestling world
T-Rex and Muscle Sam: Big Trouble in Smashing Potatoes Federation is an adventure game with a classic point-and-click interface. It uses a verbcoin-system for the interaction. When a character or an object is clicked, a coin interface appears with the actions "talk", "use" and "look". The game was a pilot for a comic series on the wrestling world. The supported languages are English and Italian. -
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The Open Protocol for Access Control Identification and Ticketing with privacY, is a standard suite of Key Establishment and Authentication protocols based on ECC and AES, for optimized contactless transactions and simple PKI based Key management.
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A program similar to Microsoft's 'net group' command for Administrators who want a list of users who are members of a global security group, but with an output suitable for scripting.
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Some features are lacking in the 'ES'-compiler for Serious Sam. Here we try to fix them. An '#include' for inside ES itself is the first project, but there may be more.
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