SAM (Sequence Alignment/Map) is a flexible generic format for storing nucleotide sequence alignment. SAMtools provide efficient utilities on manipulating alignments in the SAM format. The main samtools source code repository moved to GitHub in March 2012. For ongoing development since then, see http://github.com/samtools/samtools
The UFRaw (Unidentified Flying Raw) is a tool for reading and manipulating raw images from digital cameras. It supports most of the existing raw formats (any format supported by DCRaw). UFRaw can be used on its own or as a Gimp plug-in.
utility to split mp3, ogg vorbis and FLAC files without decoding
mp3splt is a free utility to split mp3, ogg vorbis and FLAC files without decoding, selecting begin/end time; if file is an album, you can get splitpoints automatically from internet or a local cue, cddb file. It also splits Mp3Wrap and AlbumWrap archives. Supports splitting and trimming by silence detection. For mp3 files, both ID3v1 and ID3v2 are supported using original tags or user defined tags.
Audio and video streams generator
Audio toolkit for streaming, aiming at complex Internet radio and video systems. Our stream generator is highly extensible and flexible. Script based, it can be a fully automatic daemon streamer, but is also used for live shows with an user-friendly GUI.
Open Source Solid Modeling CAD
BRL-CAD is a powerful cross-platform constructive solid geometry solid modeling system that includes an interactive geometry editor, ray-tracing for rendering & geometric analyses, network distributed framebuffer support, image & signal-processing tools.
A CPU miner for Litecoin, Bitcoin, and other cryptocurrencies
cpuminer is a multi-threaded, highly optimized CPU miner for Litecoin, Bitcoin, and other cryptocurrencies. Currently supported algorithms are SHA-256d and scrypt(N, 1, 1). It supports the getblocktemplate mining protocol as well as the Stratum mining protocol, and can be used for both solo and pooled mining. Notice: Please see here to understand why this package is recognized as a threat by some antivirus software: https://github.com/pooler/cpuminer/issues/13
A comprehensive software suite for reading barcodes. Supports EAN/UPC, Code 128, Code 39, Interleaved 2 of 5 and QR Code. Includes libraries and applications for decoding captured barcode images and using a video device (eg, webcam) as a barcode scanner.
Swiss army knife of image processing
GraphicsMagick provides a set of commandline tools and programming APIs for manipulating, editing, and converting raster and vector images. It is derived from ImageMagick, with the objective of providing better stability and performance than ImageMagick while retaining the original MIT/X11 license.
RHash is a console utility for computing and verifying hash sums of files. It supports CRC32, MD4, MD5, SHA1, SHA256, SHA512, SHA3, Tiger, TTH, Torrent BTIH, AICH, ED2K, GOST R 34.11-94, RIPEMD-160, HAS-160, EDON-R 256/512, WHIRLPOOL and SNEFRU hash sums.
Advanced Onion Router is a portable client for the OR network and is intended to be an improved alternative for Tor+Vidalia+Privoxy bundle for Windows users. Some of the improvements include UNICODE paths, support for HTTP and HTTPS proxy protocols on the same Socks4/Socks5 port with HTTP header filtering that generates fake identity-dependent headers every time the identity is changed (proxy chains are also supported), support for NTLM proxies, a User Interface that makes Tor's options and actions more accessible, local banlist for forbidden addresses, private identity isolation, a point-and-click process interceptor that can redirect connections from programs that don't support proxies, also giving them fake information about the local system and support for .onion addresses. Also, it can estimate AS paths for all circuits and prevent AS path intersections, it can restrict circuits to be built using only nodes from different countries, can change circuit lengths and more.
SDCC is a retargettable, optimizing standard C (ANSI C89, ISO C99, ISO C11) compiler that targets a growing list of processors including the Intel 8051, Maxim 80DS390, Zilog Z80, Z180, Rabbit 2000, gbz80, Motorola 68HC08, S08 and STMicroelectronics STM8 targets. There also is incomplete support for the Microchip PIC16 and PIC18.
A very high quality package of printer drivers for CUPS on Linux, Macintosh OS X, and other POSIX-compliant operating systems. This project also maintains an enhanced Print plug-in for GIMP 2.x from the same code base.
Command line tool for managing Amazon S3 and CloudFront services
Open-source tool to access Amazon S3 file storage. S3cmd is a free command line tool and client for uploading, retrieving and managing data in Amazon S3 and other cloud storage service providers that use the S3 protocol, such as Google Cloud Storage. Lots of features and options have been added to s3cmd since its very first release in 2008.... we recently counted more than 60 command line options, including multipart uploads, encryption, incremental backup, s3 sync, ACL and Metadata management, S3 bucket size, bucket policies, and more!
GeographicLib is a small set of C++ classes for converting between geographic, UTM, UPS, MGRS, and geocentric coordinates, for gravity (e.g., EGM2008), geoid, and geomagnetic field (e.g., WMM2010) calculations, and for solving geodesic problems. For documentation, visit https://geographiclib.sf.io
FLAC is a free lossless compressed audio format which supports streaming and archival. The FLAC project maintains the format and provides a reference encoder/decoder and input plugins for several popular audio players.
A barcode encoding library supporting over 50 symbologies.
Encodes data into any of the following: Australia Post barcode, Aztec Code, Aztec Runes, Channel Code, Codabar, Codablock-F, Code 11, Code 128, Code 16K, Code 2 of 5 (Including IATA, Datalogic, ITF14, Deutsche Post Leitcode and Identcode), Code 32 (Italian Pharmacode), Code 39, Code 39+, Code 49, Code 93, Code One, Data Matrix (ECC200), DotCode, Dutch Post KIX, EAN, Grid Matrix, GS-1 DataBar, Han Xin Code, HIBC, Japan Post, Korea Post, LOGMARS, MaxiCode, MSI, PDF417 and Micro PDF417, Pharmacode, POSTNET, PLANET, QR Code and Micro QR, Royal Mail 4-state (RM4SCC) and Mailmark, Telepen, UPC-A and UPC-E, UPNQR and USPS Intelligent Mail. Also supports full range of Unicode (UTF8) input using automated ECI switching for encoding in multiple languages and GS-1 data input mode. Save to PNG, BMP, TIF, GIF, PCX, SVG, WMF and EPS output file formats. Includes CLI and GUI interfaces and fully documented API for integrating with other projects.
PDF transformation/manipulation program + library
QPDF is a C++ library and set of programs that inspect and manipulate the structure of PDF files. It can encrypt and linearize files, expose the internals of a PDF file, and do many other operations useful to end users and PDF developers.
BWA is a program for aligning sequencing reads against a large reference genome (e.g. human genome). It has two major components, one for read shorter than 150bp and the other for longer reads.
Home of the Open Object Rexx Project. ooRexx is the open source version of IBM's Object REXX Interpreter. It is upwardly compatible with classic REXX and will execute classic REXX programs unchanged. The project is managed by the Rexx Language Assoc.
cross-distribution software installation system
Zero Install is a decentralised cross-distribution software installation system. Create one package that works everywhere! With dependency handling and automatic updates, full support for shared libraries, and integration with native package managers
A free COBOL compiler
GnuCOBOL (formerly OpenCOBOL) is a free COBOL compiler. cobc translates COBOL source to executable using intermediate C, designated C compiler and linker. OpenCOBOL 1.1 became GNU Cobol 1.1 in 2013. GnuCOBOL 2.2 is the latest, version 3.0 is on its way. A programmer's guide, by Gary Cutler and Vincent Coen, is indexed at https://open-cobol.sourceforge.io together with more documentation. OpenCOBOL was written by Keisuke Nishida and Roger While, from 2001 to 2012. GnuCOBOL is also authored by Simon Sobisch, Ron Norman, Edward Hart, Sergey Kashyrin, Dave Pitts and Brian Tiffin. Others listed in the AUTHORS and THANKS files. Copyright 2001-2018 Free Software Foundation, Inc. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the FSF; either version 3, or (at your option) any later version. The libcob run time support source tree is licensed LGPL.
This project manages the libraries, configuration, and diagnostic tools for Wacom tablets running under Linux. It also maintains updated Linux kernel drivers and Xorg/XFree86 XInput drivers.
Ganglia is a scalable distributed monitoring system for high-performance computing systems such as clusters and Grids. It is based on a hierarchical design targeted at federations of clusters. Supports clusters up to 2000 nodes in size.
Creates APNG animation from PNG/TGA image sequence.
Creates highly optimized Animated PNG files from PNG/TGA image sequences. CLI versions available for all major OSes. GUI versions for Windows and macOS. Also, APNG Disassembler can be found at http://sourceforge.net/projects/apngdis
Banish crusty code with the Uncrustify C/C++/C#/D/Java/Pawn source code beautifier. It indents, adds newlines, aligns, etc, and is highly configurable.