Search Results for "aligner"
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Showing 29 open source projects for "aligner"
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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. -
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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... -
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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... -
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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.
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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. -
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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.
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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... -
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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... -
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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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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.
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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... -
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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), -
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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... -
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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...
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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. -
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SOAP3-DP
Fast, Accurate and Sensitive GPU-based Short Read Aligner
... with different lengths. SOAP3-dp natively supports BAM file format and provides the same scoring scheme as BWA, which enables it to be integrated into existing analysis pipelines. Citation: Luo R, Wong T, Zhu J, Liu C-M, Zhu X, et al. (2013) SOAP3-dp: Fast, Accurate and Sensitive GPU-Based Short Read Aligner. PLoS ONE 8(5): e65632. doi:10.1371/journal.pone.0065632 -
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InMethyl
Design of target-specific primers for bis. sequencing of CpG-islands
InMethyl is a Python-based application for the design of target-specific primer combinations for PCR amplification and bisulfite sequencing of complete CpG-islands. InMethyl uses bowtie high-throughoutput aligner to identify potential mis-priming sites in the bisulfite treated or intact genome and then – undesirable potential PCR products. InMethyl provides a balance between various characteristics that allows to pick up primers in hard-to-study genomic regions. This balance is based... -
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CUSHAW2: Parallel Gapped Read Alignment
One of the leading short-/long-read aligner to large genomes
CUSHAW2 is a fast and parallel gapped read alignment to large genomes, such as the human genome. The performance evaluation, by aligning simulated and real datasets to the human genome, shows that CUSHAW2 is consistently among the highest-ranked aligners in terms of alignment quality for both single-end and paired-end alignment, while demonstrating highly competitive speed. Furthermore, our aligner shows good parallel scalability with respect to the number of CPU threads. -
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HBSAnalyzer
Aligner and methylation caller for hairpin bisulfite sequencing data
HBS Analyzer is a methylation calling tool for hairpin-bisulfite sequencing data. HBS Analyzer can accept raw hairpin-bisulfite sequencing data in FASTA or FASTQ format, align the paired end reads to the reference genome and call methylation. Given the double stranded nature of the data that is used, HBS analyzer can identify errors caused by PCR and sequencing along with identifying hemi-methylated sites. This error information is also considered while making the methylation call and hence... -
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HBSAnalyzer
Aligner and methylation caller for hairpin bisulfite sequencing data
HBS Analyzer is a methylation calling tool for hairpin-bisulfite sequencing data. HBS Analyzer can accept raw hairpin-bisulfite sequencing data in FASTA or FASTQ format, align the paired end reads to the reference genome and call methylation. Given the double stranded nature of the data that is used, HBS analyzer can identify errors caused by PCR and sequencing along with identifying hemi-methylated sites. This error information is also considered while making the methylation call and hence... -
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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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t2t-pipe
automatic alignment pipeline for parallel treebanks
The *Tree-to-Tree (t2t) Alignment Pipe* is a collection of python scripts, co-ordinating the process of automatic alignment of parallel treebanks from plain text files with a single call from a unix command line. Supported Languages: DE, FR, EN -
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Ferox
Ferox - Sequence Alignment with Fuzzy K-mers
Ferox is a DNA sequence alignment application that uses fuzzy k-mers to quickly and accurately align sets of sequence reads against a reference genome. Ferox can also be used to align whole genomes. The seeding mechanism used by Ferox is highly configurable, allowing custom fuzzy seeds to be created declaratively in an XML configuration file. -
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CUSHAW: CUDA-based Short Read Alignment
the first aligner introducing a complete paired-end alignment on GPUs
CUSHAW is a CUDA compatible short read aligner to large genomes, such as the human genome, based on the Burrows Wheeler transform.