Search Results for "alignment"
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Showing 45 open source projects for "alignment"
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Zen Kernel
Zen Patched Kernel Sources
Zen Patched Kernel Sources. This is the top level of the kernel’s documentation tree. Kernel documentation, like the kernel itself, is very much a work in progress; that is especially true as we work to integrate our many scattered documents into a coherent whole. ARC processors are highly configurable and several configurable options are supported in Linux. Some options are transparent to software (i.e cache geometries, some can be detected at runtime and configured and used accordingly,... -
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kallisto
Near-optimal RNA-Seq quantification
kallisto is a program for near-optimal quantification of transcript abundances from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the idea of using pseudoalignment to quickly determine reads and targets’ compatibility, with no need for alignment. According to benchmarks done on a Mac desktop computer, kallisto can quantify 30 million human bulk RNA-seq reads in less than 3 minutes with just the read sequences and a transcriptome index, that in itself can take more than 10 minutes to build. And since it uses pseudoalignment, it is robust to errors in the reads and preserves the key information needed for quantification. ... -
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txiki.js
A tiny JavaScript runtime
txiki.js is a lightweight and modern JavaScript runtime designed to provide a compact yet powerful alternative to larger runtimes like Node.js and Deno. It is built on top of QuickJS-ng as its JavaScript engine and uses libuv for asynchronous I/O and system-level operations, allowing it to support a wide range of platform capabilities. The runtime aims to implement modern ECMAScript standards while aligning with WinterCG specifications, making it suitable for both server-side and scripting... -
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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
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Subread
High-performance read alignment, quantification and mutation discovery
The Subread software package is a tool kit for processing next-gen sequencing data. It includes Subread aligner, Subjunc exon-exon junction detector and featureCounts read summarization program. Subread aligner can be used to align both gDNA-seq and RNA-seq reads. Subjunc aligner was specified designed for the detection of exon-exon junction. For the mapping of RNA-seq reads, Subread performs local alignments and Subjunc performs global alignments. Subread and Subjunc were published in... -
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FFTW++ is a C++ header class for the FFTW Fast Fourier Transform library that automates memory allocation, alignment, planning, wisdom, and communication on both serial and parallel (OpenMP/MPI) architectures. In 2D and 3D, hybrid dealiasing of convolutions substantially reduces memory usage and computation time. Wrappers for C, Python, and Fortran are included.
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fanplayer
A portable video player based on ffmpeg for windows and android
...It supports a wide range of media formats and streaming protocols while maintaining low CPU and memory usage compared to traditional FFmpeg players. The architecture emphasizes synchronization accuracy, ensuring smooth playback and stable audio-video alignment. fanplayer also includes advanced playback controls such as variable speed and frame stepping. Overall, it serves as both a functional player and a reference implementation for building efficient multimedia applications. -
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...These are now hosted by the github.com/Portmidi/ project, where you can find the lastest versions of PortMidi, portsmf (Standard MIDI File support and more), and see github.com/rbdannenberg/scorealign for MIDI and/or Audio score alignment.
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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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LCUI
A small C library for building user interfaces with C, XML and CSS.
LCUI is a freely available software library to create GUI application, it is written in C, support the use XML and CSS describe the graphical interface, you can use it to make some simple effects. The above description and screenshots is for the version 1.0.0 (+), and the 1.0.0 version is still in development, it is not officially released, please do not use old versions of "files "page to download as version 1.0.0. -
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An open-source software aimed at unsupervised molecular alignment
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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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SUPERmerge
ChIP-seq coverage island analysis algorithm for broad histone marks
SUPERmerge is a ChIP-seq read pileup analysis and annotation algorithm for investigating alignment (BAM) files of diffuse histone modification ChIP-seq datasets with broad chromatin domains at a single base pair resolution level. SUPERmerge allows flexible regulation of a variety of read pileup parameters, thereby revealing how read islands aggregate into areas of coverage across the genome and what annotation features they map to within individual biological replicates. -
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AKtoolbox
Matlab Toolbox for coevolution analysis of multiple sequence alignment
AK Toolbox is a Matlab Toolbox for co-evolution analysis for protein Multiple Sequence Alignment (MSA) distributed under Simplified BSD License. The aim of AK toolbox is to provide a set of Matlab functions, which are independent of Matlab Bioinforamtics Toolbox, for coevolution anaylsis for MSA. At present, co-evolution methods available in this package are Statistical Coupling Analysis (SCA), Explicit Likelihood of Subset Covariance (ELSC), Mutual Information (MI), Observed Minus Expected Square method (OMES), McLanhlan Based Substitution Correlation (MCBASC), Direct-coupling analysis (DCA) and logR. ... -
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SPRITE
Parallel SNP detection pipeline
SPRITE is an open-source software package providing a parallel implementation of the Single Nucleotide Polymorphisms (SNP) detection genomic data analysis workflow. It consists of three tools: PRUNE for read alignment, SAMPA for intermediate file processing, and PARSNIP for parallel SNP calling. -
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Fast Alignment Search Tool suite. A fast sequence read mapper suite for short reads generated with the Illumina platform. Joint development by University of Washington and Simon Fraser University
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Fast Alignment Search Tool suite. A fast sequence read mapper suite for short reads generated with the Illumina platform. Contains mrFAST and mrsFAST. Joint development by University of Washington and Simon Fraser University
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dna-bison
Bisulfite alignment On Nodes of a cluster
Bison allows users with access to a computer cluster to rapidly align whole-genome bisulfite sequencing or RRBS reads. It can align both directional and non-directional libraries and uses bowtie2. Multiple compute nodes are not absolutely required, but will make the alignment process faster. Further details available on the Wiki page. Help also available on SEQanswers (http://seqanswers.com/forums/showthread.php?t=31314) or by creating a ticket here. You can now track the development on github (https://github.com/dpryan79/bison). There is now a tutorial available in the downloads here: http://sourceforge.net/projects/dna-bison/files/bison_tutorial.tar.gz/download . -
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PlaTypUS
Plasmodium Typing Utility Software
The goal of PlaTypUS is to establish a unified Plasmodium whole genome analysis tool, that aligns short read sequences in an agreed upon manner, with many quality control steps, and calls both SNVs and CNVs in a community agreed standard way. We also seek to provide this analysis in a stand-alone graphic user interface so that labs around the world can analyze their own whole genome sequencing data, rather than relying on outside institutes. -
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DNAA is the DNA analysis package, for analyzing next-generation post-alignment whole genome resequencing data. Specifically, DNAA is able to find structural variation, SNP and indel variants, as well as evaluating the mapping and data quality.
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MSA-CUDA: multiple sequence aligner
multiple sequence alignment on CUDA-enabled GPUs.
This project is not active any more since we failed to get the permit from the Clustal team to distribute our software. You can refer to the paper "Yongchao Liu, Bertil Schmidt, Douglas L Maskell:MSA-CUDA: multiple sequence alignment on graphics processing units with CUDA. ASAP 2009" for more details. -
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hwk
hwk is a tool used for wireless lan pentests
hwk is an easy-to-use application used to attack and discover wireless networks. It's providing various modes such as authentication/deauthentication flood, beacon and probe response fuzzing. -
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NeedlemanWunsch
Fast global sequence alignment for the masses!
MOVED TO GITHUB: https://github.com/noporpoise/seq-align Global optimal sequence alignment using the Needleman-Wunsch algorithm. Aligns DNA, RNA, protein sequence and more! See our sister project local alignment using Smith-Waterman: http://sourceforge.net/projects/smithwaterman/ -
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Multiple Alignment Manipulator
MaM processes and manipulates multiple sequence alignments.
...MaM computes the exact locations of common repeat elements in multiple aligned sequences, provided by a variety of user identified programs databases and tables. It then graphically displays how the alignment quality varies throughout the aligned sequences, providing separate displays for the repeat and non-repeat portions. -
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tisa - Tab Indent Space Align
A program that will correct both indentation and alignment.
