Search Results for "assembly" - Page 2
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Showing 263 open source projects for "assembly"
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yafu
Automated integer factorization
Check yafu on github for the latest code. YAFU (with assistance from other free software) uses the most powerful modern algorithms (and implementations of them) to factor input integers in a completely automated way. The automation within YAFU is state-of-the-art, combining factorization algorithms in an intelligent and adaptive methodology that minimizes the time to find the factors of arbitrary input integers. Most algorithm implementations are multi-threaded, allowing YAFU to fully... -
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MANTI.pl / muda.pl
muda.pl - MQ unified data assembler
...The central anchor for the data congregation is the modificationSpecificPeptides.txt file - additional data is inferred from different other source files from the MaxQuant txt folder but the starting point for the data assembly is solely the modificationSpecificPeptides.txt file. Maybe also useful for normal proteomics purposes but this script is heavily optimized for protein neo-termini identification and validation. For a more thorough explanation of script parameters and evaluation strategy, please consult the extensive manual PDF. -
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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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A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows.
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ScaffCC
Compilation and optimization framework for the Scaffold language
...It is for the purpose of writing and analyzing code for quantum computing applications. ScaffCC enables researchers to compile quantum applications written in Scaffold to a low-level quantum assembly format (QASM), apply error correction, and generate time and area metrics. It is written to be scalable up to problem sizes in which quantum algorithms outperform classical ones, and as such provide valuable insight into the overheads involved and possible optimizations for a realistic implementation on a future device technology. -
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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.
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CLISP is a portable ANSI Common Lisp implementation and development environment by Bruno Haible. Interpreter, compiler, debugger, CLOS, MOP, FFI, Unicode, sockets, CLX. UI in English, German, French, Spanish, Dutch, Russian, and Danish.
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biOP
biOP [bio~ObjectPascal/bio~Delphi] bioinformatics libraries
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crAss
crAss: comparative metagenomics by cross-assembly
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FastFlow: programming multi-core
Pattern-based multi/many-core parallel programming framework
FastFlow is a C/C++ programming framework supporting the development of pattern-based parallel programs on multi/many-core, GPUs and distributed platforms. FastFlow run-time is built upon non-blocking threads and lock-free queues. Thanks to its very efficient CAS-free communication/synchronization support (e.g. few clock cycles core-to-core latency), FastFlow effectively supports the exploitation of fine grain parallelism, e.g. parallel codes managing very high frequency streams on... -
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Meraculous-2D
Eukaryotic Genome Assembler
...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. The assembly is driven by a perl pipeline which performs data fragmentation and load balancing, as well as submission and monitoring of multiple task arrays on a GE/SLURM-type cluster or a standalone multi-core server. Manuscripts in submission: https://arxiv.org/abs/1703.09852 https://arxiv.org/abs/1608 -
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A scheme (lisp) interpreter written in ARM assembly language (currently: Cortex-M4F,M7, Cortex-A5,A8,A9, Cortex-A53; previously:ARM7TDMI, ARM920T, Cortex-M3) for education, robotics, wearable devices. Tested on Allwinner A64, Amlogic S905, Atmel SAMA5D4, SAME70, SAMV71, NXP LPC4300, RT1050, iMX8M, Samsung S5P6818, ST STM32F4, STM32F7, and TI AM3359, OMAP3530, DM3730, OMAP4430, TM4C1294 chips (previously: NXP LPC-1300,1700,2000, ATMEL AT91SAM7, STM STR711, STR911, STM32, CIRRUS EP9302, LMI LM3S1968, TI OMAP).
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Genobuntu
Genobuntu Package for Next Generation Sequencing
...Therefore, Genobuntu offers a well-tailored environment for both novices and experts working in the field of genome assembly. -
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Taxoblast
Taxoblast is a pipeline to identify contamination in genomic sequence
...Scaffolds that exclusively match potential contaminants may be safely removed while sequences matching partially contaminants and partially the target organism may constitute horizontal transfers or assembly artifacts and need to be examined manually. -
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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.
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Freemat is an interpreted, matrix-oriented development environment for engineering and scientific applications, similar to the commercial package MATLAB. Freemat provides visualization, image manipulation, and plotting as well as parallel programming.
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Scripted Roulette
Simulation tool for the casino game Roulette
Scripted Roulette is an original application which helps you to develop and analyze new betting strategies for the casino game Roulette. Learn and understand more about the chances you really have to win. -
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Java bio-informatics library to analyze and convert genomic sequence and assembly data. This library was created and used by the J. Craig Venter Institute (JCVI)
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SoftIB Serial Communicator
UART communications with data flow monitoring
A simple to use serial communication software for communicating with other serial, MCU and Arduino. The SoftIB Serial Communicator communicates with other Serial devices that use a simple asynchronous communication using only the RX and TX signals without any control signals. The application was developed based on the communication with microcontrollers, but it can be used in all other cases. -
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Speakable Programming for Every Language
Your language to speak with all.
This project has the language data for spel, the main new codebase is at: https://gitlab.com/liberit/pyac A computer programming language using human language syntax for human-to-human and human-to-computer communication with high precision, supporting many languages. Currently has alpha prototype support for analytic versions of the UN languages English, Mandarin Chinese, Spanish, Arabic, Russian... -
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QSdpR
Viral Quasispecies Reconstruction software based on QSdpR algorithm
This is a viral quasispecies reconstruction software for quasispecies assembly problem on mRNA viruses, which is based on a correlation clustering approach and uses semidefinite optimization framework. The software accepts a reference genome, a NGS read set aligned to this reference and set of SNP locations in the form of a vcf file and outputs an optimal set of reconstructed species genomes which describes the underlying viral population. -
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metasort
A metagenome assembler by reducing microbial community
...Through extensive evaluations on simulated dataset, salivary and gut microbiomes, we demonstrated that metaSort has an excellent and unbiased performance on genome recovery and assembly. -
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ETHA
Hybrid Illumina/PacBio assembly of Plasmodium falciparum var genes
ETHA is a software package for hybrid assembly of Plasmodium falciparum var genes from Illumina and PacBio sequencing data -
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ViralFusionSeq [VFS]
Accurately discover viral integration events and fusion transcripts
...https://hpc.nih.gov/apps/ViralFusionSeq/ ViralFusionSeq (VFS) is a versatile high-throughput sequencing (HTS) tool for discovering viral integration events and reconstruct fusion transcripts at single-base resolution. VFS combines soft-clipping information, read-pair analysis, and targeted de novo assembly to discover and annotate viral-human fusion events. A simple yet effective empirical statistical model is used to evaluate the quality of fusion breakpoints. Minimal user defined parameters are required. Source code with user manual and installation guide of VFS is available at sourceforge's "Files" section. Citation: http://www.ncbi.nlm.nih.gov/pubmed/ -
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PBSuite
Software for Long-Read Sequencing Data from PacBio
This currently hosts two projects created and maintained by Adam English. PBJelly - the genome upgrading tool. PBHoney - the structural variation discovery tool Both are contained within the PBSuite code found in downloads. ----- PBJelly ----- Read The Paper http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047768 PBJelly is a highly automated pipeline that aligns long sequencing reads (such as PacBio RS reads or long 454 reads in fasta format) to...
