Search Results for "aligner"
Sort By:
Showing 61 open source projects for "aligner"
View related business solutions-
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.
-
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
amrlib
A python library that makes AMR parsing, generation and visualization
... in both the GUI and as library functions. Training and test code for both the StoG and GtoS models. A SpaCy extension that allows direct conversion of SpaCy Docs and Spans to AMR graphs. Sentence to Graph alignment routines FAA_Aligner (Fast_Align Algorithm), based on the ISI aligner code detailed in this paper. RBW_Aligner (Rule Based Word) for a simple, single token to single node alignment. -
4
BBMap
BBMap short read aligner, and other bioinformatic tools.
This package includes BBMap, a short read aligner, as well as various other bioinformatic tools. It is written in pure Java, can run on any platform, and has no dependencies other than Java being installed (compiled for Java 6 and higher). All tools are efficient and multithreaded. BBMap: Short read aligner for DNA and RNA-seq data. Capable of handling arbitrarily large genomes with millions of scaffolds. Handles Illumina, PacBio, 454, and other reads; very high sensitivity and tolerant... -
Our intuitive email marketing software to help you save time and build lasting relationships with your subscribers.
-
5
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.
-
6
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... -
7
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. -
8
Lung cancer screening panel
Software for predicting probability of lung cancer from VCF file
We have developed a lung cancer screening panel based on the occurrence of specific clonal hematopoietic mutations in peripheral blood samples. The software provided here can be used to predict the probability of cancer from peripheral blood samples. The sequencing data from the blood sample should be first aligned to the GRCh38 reference genome using the Burroughs-Wheeler aligner and variants called using the Mutect2 for variant calling. The resulting VCF file is used as input to the software... -
9
-
Built for growing businesses and well-established enterprises alike, Multiview is a highly scalable and robust ERP.
-
10
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.
-
11
monolingual-sentence-aligner
Monolingual Sentence Aligner
... 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 -
12
-
13
Satsuma
Whole-genome synteny alignments
Satsuma is a whole-genome synteny aligner based on the Fast Fourier Transform and a battleship-style search. Parallelization is built-in. Grabherr, M. G., Russell, P., Meyer, M., Mauceli, E., Alföldi, J., Di Palma, F., & Lindblad-Toh, K. (2010). Genome-wide synteny through highly sensitive sequence alignment: Satsuma. Bioinformatics, 26(9), 1145-51. For more information, documentation and recent activity, please check out our project web page: http://satsuma.sourceforge.net/ -
14
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.
-
15
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, number of... -
16
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... -
17
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... -
18
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. -
19
AC-DIAMOND is a DNA-protein aligner. The source code of AC-DIAMOND can be found here: https://github.com/Maihj/AC-DIAMOND
-
20
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... -
21
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.
-
22
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... -
23
-
24
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), -
25
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...