Search Results for "aligner"
Sort By:
Showing 46 open source projects for "aligner"
View related business solutions-
Red Hat Enterprise Linux (RHEL) on Microsoft Azure provides a secure, reliable, and flexible foundation for your cloud infrastructure. Red Hat Enterprise Linux on Microsoft Azure is ideal for enterprises seeking to enhance their cloud environment with seamless integration, consistent performance, and comprehensive support.
-
HubSpot is an AI-powered customer platform with all the software, integrations, and resources you need to connect your marketing, sales, and customer service. HubSpot's connected platform enables you to grow your business faster by focusing on what matters most: your customers.
-
1
LF Aligner helps translators create translation memories from texts and their translations. It relies on Hunalign for automatic sentence pairing. Input: txt, doc, docx, rtf, pdf, html. Output: tab delimited txt, TMX and xls. With web features. My email address is listed in readme.txt; for support, use the forum here. My personal website: www.farkastranslations.com.
-
2
Tokenized Text Aligner
Aligns tokens in two versions of a text with differing tokenization.
.... In its default implementation, it produces a human-readable CSV table associating tokens in text A with tokens in text B, and can also inject token-level annotation from text B to text A. The Aligner class on which the default implementation is based can be incorporated into more complex workflows. -
3
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... -
4
Bowtie, an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers. Please cite: Langmead B, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25.
-
BackBox seamlessly integrates with network monitoring and NetOps platforms and automates configuration backups, restores, and change detection. BackBox also provides before and after config diffs for change management, and automated remediation of discovered network security issues.
-
5
OmegaT - multiplatform CAT tool
The free computer aided translation (CAT) tool for professionals
OmegaT is a free and open source multiplatform Computer Assisted Translation tool with fuzzy matching, translation memory, keyword search, glossaries, and translation leveraging into updated projects. -
6
miRDeep*
MiRDeep*
Please cite: An, J., Lai, J., Lehman, M.L. and Nelson, C.C. (2013) miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data. Nucleic Acids Res, 41, 727-737. We will create index for you if you tell us your interested species (j.an@qut.edu.au). download command line version "MDS_command_line_Vxx.zip" clicking "Browse All Files" please find miRPlant in sourceforge for plant miRNA prediction. -
7
-
8
Parallel text aligner dessigned to generate transation memories (TMX files) from two files tagged with any kind of XML-based tags. The application uses the tag structure and the text blok length to perform the alignment.
-
9
monolingual-sentence-aligner
Monolingual Sentence Aligner
... with custom settings and fixing some output - process.js: The main entry, containing the general flow of processing. Please read Readme.md for more details. Github: https://github.com/nlpcl-lab/monolingual-sentence-aligner -
Don’t settle when it comes to managing your clients’ IT infrastructure. Exceed their expectations with ConnectWise RMM, our MSP RMM software that provides proactive tools and NOC services—regardless of device environment. With the number of new vulnerabilities rising each year, smart patching procedures have never been more important. We automatically test and deploy patches when they are viable and restrict patches that are harmful. Get better protection for clients while you spend less time managing endpoints and more time growing your business. It’s tough to locate, afford, and retain quality talent. In fact, 81% of IT leaders say it’s hard to find the recruits they need. Add ConnectWise RMM, NOC services and get the expertise and problem resolution you need to become the advisor your clients demand—without adding headcount.
-
10
TaBS-Pipe
Targeted Bisulfite Sequencing Data Analysis Pipeline v1.0.2
A pipeline to analyze the data obtained from targeted bisulfite sequencing through the ion-torrent platform. TaBSAP is a pipeline to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step and enables a researcher to analyze the methylation levels of their samples straight away. It's main features are: -Bisulfite mapping and methylation calling in one single step -Supports single-end read alignments -Alignment seed length,... -
11
HSRA
Hadoop spliced read aligner for RNA-seq data
HSRA is a MapReduce-based parallel tool for mapping reads from RNA sequencing (RNA-seq) experiments. RNA-seq analyses typically begin by mapping reads to a reference genome in order to determine the location from which the reads were originated, which is a very time-consuming step. This tool allows bioinformatics researchers to efficiently distribute their mapping tasks over the nodes of a cluster by combining a fast multithreaded spliced aligner (HISAT2) with Apache Hadoop, which... -
12
PARot polar aligner
Software for polar alignment of equatorial mounts
PARot is a program for ultra fast and precise polar alignment of equatorial mounts. You can easily achieve alignment accuracy better than 1 arcmin in 5 minutes of time. You take one image of the celestial pole, rotate the mount around the RA axis and take another image. The program compares the images and shows you the necessary adjustment. The adjustment process is controlled by the live-liew created by your camera. Requirements: * A computer with Windows OS (tested with WinXP x64, Win7... -
13
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.
-
14
AC-DIAMOND is a DNA-protein aligner. The source code of AC-DIAMOND can be found here: https://github.com/Maihj/AC-DIAMOND
-
15
Barracuda is a high-speed sequence aligner based on Sanger's BWA and utilizes the latest Nvidia CUDA architecture for accelerating alignments of sequence reads generated by next-generation sequencers.
-
16
BOWS
Bioinformatics Open Web Services
BOWS is a generic system based on Web Services which allows programmatic access to applications running on HPC clusters. BOWS allows incorporation of several independent applications since programmers can install them in HPC clusters in any programming language. The lonely requirement is to write a script named “arrow” which calls BOWS back-end services periodically in order to check for new processes and their required parameters. If a new process is found, the “arrow” script should change... -
17
VoltMR
Pure java NGS mapping soft run on Hadoop 2.0
ＶｏｌｔＭＲ is pure java NGS (DNA/RNA) mapping and realignment soft that run on Hadoop 2.0 The accuracy is comparable to BWA-MEM and novoalgin with speed faster than those aligner. Using 100 core, VoltMR finish typical exome sample (10GB),mapping, sort, mark duplicate, local realignment in 30 minitue. It use about 10GB to 15GB RAM for each hadoop mapper and reducer. Currently, VoltMR take fastq as a input and output bam/ADAM format. For DNA mapping, GATK compatible realignment/recalbration... -
18
-
19
erne
ERNE - Extended Randomized Numerical alignEr
We present ERNE (Extended Randomized Numerical alignEr), a short string alignment package whose goal is to provide an all-inclusive set of tools to handle short (NGS-like) reads. ERNE comprises ERNE-FILTER (read trimming and continamination filtering), ERNE-MAP (core alignment tool/algorithm), ERNE-BS5 (bisulfite treated reads aligner), and ERNE-PMAP/ERNE-PBS5 (distributed versions of the aligners), -
20
MICA-aligner
Next-generation sequencing short reads aligner based on Intel® MIC
Latest Code in GitHub: https://github.com/aquaskyline/MICA-aligner To better utilize MIC-enabled computers for NGS data analysis, we developed a new short-read aligner MICA that is optimized in view of MIC’s limitation and the extra parallelism inside each MIC core. Experiments on aligning 150bp paired-end reads show that MICA using one MIC board is ~4.85 times faster than the CPU-(multi-core)-based BWA-MEM and about the same speed as the GPU-based SOAP3-dp. Furthermore, MICA’s simplicity... -
21
LAMSA
Long Approximate Matches-based Split Aligner
LAMSA (Long Approximate Matches-based Split Aligner) is a novel split alignment approach with faster speed and good ability of handling SV events. It is well-suited to align long reads (over thousands of base-pairs). -
22
Crosscut is a set of high-quality and efficient modules handling NGS datasets in a population. Chronos is a highly sensitive and efficient multiple whole genome aligner in a population. Apollo is a structural variant caller in a population. Poseidon is a highly sensitive and efficient taxonomy classifier. All algorithms are developed since Feb. 6. 2015 by Euncheon Lim in Prof. Weigel's Lab in Max-Planck Institute for Developmental Biology.
-
23
CUSHAW3 is an open-source parallelized, sensitive and accurate short-read aligner. This aligner proposes a general approach to properly aligning both easy and hard reads to large genomes such as the human genome. Perform evaluation on alignment quality reals that CUSHAW3 consistently outperforms CUSHAW2, BWA-MEM, Bowtie2 and GEM in terms of single-end and paired-end alignment. Furthermore, our aligner has demonstrated better paired-end alignment performance than Novalign3 for short-reads...
-
24
parSRA
Portable Framework for the Parallel Execution of Short Read Aligners
... allows the users to parallelize the execution of existing SRA tools without the need to modify the source code of parSRA or the aligner. -
25