Search Results for "high-level assembler"
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Showing 10 open source projects for "high-level assembler"
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Meraculous-2D
Eukaryotic Genome Assembler
---------------------------------------- IMPORTANT: Meraculous-2D has been superseded by the HipMer assembler, available here: https://sourceforge.net/projects/hipmer/ ----------------------------------------- Meraculous-2D is a whole genome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... -
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FlexxCpu
Flexible and eXpandable Cpu simulation
A small simulation of an experimental customized Cpu called FlexxCpu. A virtual Cpu whose assembly instructions have been strongly influenced by old cpus architecture (8080, 6809, z80, 68k, etc...) Please support this project by donating to this fundraiser: ------------------------------------------- Give birth to new travel bicycles!!! https://gofund.me/2201d2a4 ------------------------------------------- -
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metasort
A metagenome assembler by reducing microbial community
Most current approaches analyze metagenomic data with the participation of reference genomes. However, novel microbial communities extend far beyond the coverage of reference databases and de novo metagenome assembly from complex microbial communities still remains a great challenge. Here we present a novel experimental and bioinformatic framework, metaSort, for effective construction of bacterial genomes from metagenomic samples. MetaSort provides a sorted mini-metagenome approach based on... -
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MaxInfo
Transcriptome assembler for RNA-seq
MaxInfo is an automated transcript discovery and quantification software designing for high-throughput RNA sequencing (RNA-seq). Assembling transcripts from reads are challenging because of the unpredictable uncertainties arising from completing full genome structure with very partial observations. MaxInfo tackles this problem by explicitly reducing the inherent uncertainties in the biological system caused by missing information. -
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SAT-Assembler
Scalable and accurate targeted gene assembly for large-scale NGS data
SAT-Assembler is a scalable and accurate gene assembly tool for large-scale RNA-Seq and metagenomic data. It recovers genes from gene families of particular interest to biologists with high coverage, low chimera rate, and extremely low memory usage compared with exiting gene assembly tools. Moreover, it is naturally compatible with parallel computing platforms. -
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SOAPdenovo-Trans
A de novo transcriptome assembler.
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. -
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PASHA: Parallelized Short Read Assembly
One of the fastest parallel short read assemblers for large genomes.
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. ... -
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Customizable Instruction Set Simulator
Customizable simulator of virtual CPU with multitasking.
...Application written in C# 4, .Net Framework 4.0 , Visual Studio 2010 Features: - IDE- like environment with MDI interface - Customizable (plug- ins) architecture: instruction sets, directives, registers, additional MDI windows - Own assembler using Intel syntax producing binary programs - Simulation of i386- like CPU operating on multi- level cache and RAM - Simulation of debugger and memory view - Features of simple OS: scheduling, multi- tasking by context switching, memory management Currently available version considered "initial". Some of features were simplified or cut out (eg. plugins were statically built into project rather than loaded dynamically) to meet the deadline. ... -
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FPGAsm
Create fast bare-metal FPGA designs without Verilog or VHDL
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. -
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...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.
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