Search Results for "assembler"

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.

Integrated Development Environment for some microcontrollers based on 8051(e.g. AT89S8253). Supported languages are Assembly and C. It has its own simulator, assembler, editor and many other tools. See the project web site for more details and the newest updates.

MIRA V5 is available only on GitHub! The V4 version released here on SourceForge stay up as some automated release fetching packages rely on V4. MIRA - Sequence assembler and sequence mapping for whole genome shotgun and EST / RNASeq sequencing data. Can use Sanger, 454, Illumina and IonTorrent data. PacBio: CCS and error corrected data usable, uncorrected not yet.

---------------------------------------- IMPORTANT: Meraculous-2D has been superseded by the HipMer assembler, available here: https://sourceforge.net/projects/hipmer/ ----------------------------------------- Meraculous-2D is a whole genome assembler for NGS reads (Illumina) that is capable of assembling large, diploid genomes with modest computational requirements. Features include: - Efficient k-mer counting and deBruijn graph traversal - Two modes of handling of diploid allelic variation - Improved scaffolding that produces more complete assemblies without compromising scaffolding accuracy. ...

Celera Assembler (CA) is a whole-genome shotgun (WGS) assembler for the reconstruction of genomic DNA sequence from WGS sequencing data.

...A nucleotide assembly-based strategy does not fare much better since metagenomic assemblies are typically very fragmented and also leave a large fraction of reads unassembled. We present a method for reconstructing complete protein sequences directly from NGS metagenomic data. Our framework is based on a novel Short Peptide Assembler (SPA) that assembles protein sequences from their constituent peptide fragments identified on short reads. We also present a new implementation of SPA based on suffix array (SFA-SPA) which runs significantly faster than SPA. Youngik Yang, Cuncong Zhong, and Shibu Yooseph* J. Craig Venter Institute, San Diego, CA {yyang,czhong,syooseph}@jcvi.org * Corresponding author SPA is available in binary on 64 bit Linux OS. ...

Latest Codes on GitHub: https://github.com/aquaskyline/SOAPdenovo-Trans SOAPdenovo-Trans is a de novo transcriptome assembler inherited from the SOAPdenovo2 framework, designed for assembling transcriptome with alternative splicing and different expression level. The assembler provides a more comprehensive way to construct the full-length transcript sets compare to SOAPdenovo2.

PASHA is a parallel short read assembler for large genomes using de Bruijn graphs. Taking advantage of both shared-memory multi-core CPUs and distributed-memory compute clusters, PASHA has demonstrated its potential to perform high-quality de-novo assembly of large genomes in reasonable time with modest computing resources. Our evaluation using three small real paired-end datasets shows that PASHA is able to produce better assemblies with comparable genome coverage and mis-assembly rates compared to three leading assemblers: Velvet, ABySS and SOAPdenovo. ...

lilpM32 is a MIPS-like processor designed in Logisim, assembler program and documentation for them. Complete assembler and fully functional instruction set with I/O and subroutines features allow to write full-blown complicated programs.

FPGAsm is a low-level alternative to verilog and VHDL. A near-instant 'assembler for FPGAs', this simple yet powerful language facilitates bottom-up design, layout and wiring of modules, and generation of .xdl output. With about 10 keywords to learn, you can start making circuits in minutes. Now you can focus on learning the ins and outs of the FPGA instead of complex tools and languages. Fast turnaround time and bottom-up approach invite exploration, experimentation, live circuit testing and physical test harness creation, radically changing the workflow. ...

...A key design objective is to use as little dedicated hardware as possible for communication between nodes in the network, and to be able to adapt the network topology in real-time so as to minimize the occurrence of collisions between packets. To achieve this, a protocol has been designed specifically for the task, and implemented in assembler for AVR microcontrollers. The project is currently at the stage of testing the protocol for bugs and implementing some simple devices which use it.

This is an attempt to write a CPU emulator in Trolltech QT 4.4. Basic Functionality: - 8 bit registers - Self-composed instructoin set (in progress) - Data and Assembler Editor / parser (not started) - Text and graphical input / output (not started

...It has built in 14 different iterate {Mandelbrot) functions. Many possibilities for changing parameters, saving as bitmap or small file. windows-32. Linux 32 - 64bit. Low level written in assembler.

OCR c++ library of computer optical recognition methods. In library: contour recognition; contour vectorisation; matrix letters feature recognition; web based GUI; assembler core on SS3 instruction; xml support; detect page rotation and segmentation;

Pes is an simple programing language. It has just few basic constructions and it has c-like & pascal-like syntax. The compiler output is Jasmin - an assembler for java virtual machine. It was my school project.

MEDDAC is the seeding point for designing a new approach to Operating System design itself. It is an Open Source project with roots in mainframe design and development the author began in 1979. Monitor Editor Disassembler Decompiler Assembler Compiler

BorgASM will be a fully integrated environment for simulated cybernetic and robotic experimentation. A general purpose real-time AI/physics/animation engine core will facilitate virtual exploration of the unification of man and machine.

MOPPI (Multiple OPerations Per Instruction) is a simple machine simulator written in C++. It will include assembler, loader, and simulator components that allow a user to experience the entire process of developing a simple microprocessor based simulator

An open source set of embedded software libraries in C, C++ and Assembler for robotics programming, targeting controllers using Motorola's 16 bit controllers, concentrating on the 6811 and 6812. Development of a common development toolset.

kasm is an assembler for the Saturn microprocessor, used in the HP48/HP49 calculators. It uses MASD syntax, which has only very small incompatibilities with the traditional syntax, supports a few constructs that make the assembly language be closer to a

GROKI is an OpenSource-Project (GNU) that deals with Control and Programming of (small) mechanical Robots. HW: µC/MCU OS: Linux/Unix GUI: GTK PLs: C++ and Assembler

This STL-like C++ library contains classes for long integer numbers processing with using of assembler functions as a backend. Lazy evaluation is also used for optimization. It also contains generic implementation of classical number-theory algorithms.