Search Results for "ngs" - Page 2
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Showing 145 open source projects for "ngs"
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Genobuntu
Genobuntu Package for Next Generation Sequencing
Genobuntu is a software package containing more than 70 software and packages oriented towards NGS. In its current version, Genobuntu supports pre assembly tools, genome assemblers as well as post assembly tools. Commonly used biological software and example script files for different assembly pipelines have also been provided, where the example script files can be updated to suit one’s experimental needs. Genobuntu attempts to reduce the amount of time and energy needed to build software workstations and it can also act as a good teaching source for a class room setting. ... -
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Nuvarator
A SNV Detection Software Tools Installer Package
...SNV detection is range of computational tech- niques and algorithms used to identify the existence of single nu- cleotide variants (SNVs) by using the result from Next Generation Sequencing (NGS) experiments. NGS are methods employed for Whole Genome Sequencing, a process for determining the precise order of nucleotides within a DNA molecule which can improve the knowledge available to researchers interested in evolutionary biology, and hence lays the foundation for predicting disease susceptibility and drug response. ... -
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GENSENG
GENSENG is a software detecting CNVs from NGS data
GENSENG is a software detecting CNVs(Copy Number Variations) from NGS(Next Generation Sequencing) data. We have uploaded the data preparation codes. Please download it from Files folder. -
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GMcloser
Closing the gaps in scaffolds with preassembled contigs
GMcloser fills and closes the gaps present in scaffold assemblies, especially those generated by the de novo assembly of whole genomes with next-generation sequencing (NGS) reads. Unlike other gap-closing tools that use only NGS reads, GMcloser uses preassembled contig sets or long read sets as the sequences to close gaps and uses paired-end (PE) reads and a likelihood-based algorithm to improve the accuracy and efficiency of gap closure. The efficiency of gap closure can be increased by successive treatments with different contig sets. ... -
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scalpel
Genetic variants discovery tool
Bioinformatics pipeline for discovery of genetic variants from NGS reads. -
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...Schöberl: "C++11 Implementation of Finite Elements in NGSolve", ASC Report 30/2014, Institute for Analysis and Scientific Computing, Vienna University of Technology, 2014 http://www.asc.tuwien.ac.at/~schoeberl/wiki/publications/ngs-cpp11.pdf
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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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The increasing demand of next-generation sequencing (NGS) studies has remarked the necessity of integrated and reliable pipelines to analyse deep-sequencing experiments in an efficient way. We present RUbioSeq+, a stand-alone and multiplatform application for the integrated analysis of NGS data. More specifically, our software implements pipelines for the analysis of single nucleotide and copy-number variation, bisulfite-seq and ChIP-seq experiments using well-established tools to perform these common tasks. ...
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AccNET
AccNET: Accessory Genome Constellation Network.
AccNET is a Perl application that presents a new way to study the accessory genome of a given set of organisms. Using the proteomes of these organisms, AccNET create a bipartite network compatible with common network analysis platforms. AccNET collects phylogenetic and functional information in a network improving the analysis capability. Networks offer a new perspective of organism organization through elements acquired by horizontal gene transfers and not constricted by hierarchical... -
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ngs-suite
A set of NGS tools for DNA-seq and BS-seq
ngs-suite aims is to collect a set of fast and well written C++11 software to handle analysis and manipulation of NGS short reads. It works with DNA-seq and BS-seq data. -
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Short-Pair
Sensitive Short Read Homology Search for Paired-End Reads
The profi le-based homology search method designed for short reads by taking advantage of the paired-end sequencing properties. Short-Pair is designed for NGS data that lack reference genomes. -
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SPANDx
Comparative analysis of haploid next-generation genome sequence data
SPANDx is your one-stop tool for identifying SNP and indel variants in haploid genomes using NGS data. SPANDx performs alignment of raw NGS reads against your chosen reference genome or pan-genome, followed by accurate variant calling and annotation, and locus presence/absence determination. SPANDx produces SNP and indel matrices for downstream phylogenetic analyses. Annotated, genome-wide SNPs and indels can also be identified if specified, and are output in human readable format. ... -
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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. -
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PeaksAndValleys
Peaks and Valley detection using NGS data
Active regulatory elements in eukaryotic genomes are typically associated with nucleosome-depleted regions that are hypersensitive to digestion by nonspecific endonucleases. Techniques which distinguish active regulatory elements by virtue of this include micrococcal nuclease digestion of chromatin (MNAse-seq), which preferentially depletes DNA which is not tightly bound by proteins, and formaldehyde-assisted isolation of regulatory elements (FAIRE-seq), which enriches for sequences which... -
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Placnet
Placnet project
Plasmid Constellation Network project. Placnet is a new tools for plasmid analysis in NGS projects. Placnet has been written in Perl. It's been optimized to work with Illumina sequences but it also works with 454, Iontorrent or any of the actual sequence technologies. The input of placnet is a set of contigs and one or more SAM files with the mapping of the reads against the contigs. Placnet obtains a set of files, easily opened on Cytoscape software or other network tools. ... -
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P3BSseq
Parallel processing pipeline for analysis of bisulfite sequencing data
...We optimized the P3BSseq parameters for both directional and non-directional libraries, and for both single-end and paired-end reads of Whole Genome and Reduced Representation BSseq. P3BSseq is a user-friendly streamlined solution for BSseq upstream analysis, requiring only basic computer and NGS knowledge. -
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DaMold
a data mining platform for variant annotation and visualization.
...DaMold seamlessly integrates six widely used genome browser such as the UCSC genome browser, Ensembl genome browser, GWAS central genome browser, HapMap genome browser, 1000 Genomes browser, and NCBI variation viewer. Each variant is directly linked with each genome browser. DaMold can be used to analyze, elucidate, and interpret variants from data generated by NGS in clinical research. -
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Flow Solver Package with different applications (laminar flows, heat driven flows) in 3D and 2D for Netgen/NGSolve
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scFvMiner
Scripts for analysing NGS data
These scripts written in java can be used for deep sequencing analysis of the scFv antibodies from a synthetic antibody library and yields complete sequence information on the randomized areas of antibodies enriched from the library by phage display. The methods are descriped in Lövgen, J., Pursiheimo, J.P., Pyykkö, M., Salmi, J. & Lamminmäki, U. (2016) Next generation sequencing of all variable loops of synthetic single framework scFv – application in anti-HDL antibody selections. New... -
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Raw sequences produced by next generation sequencing (NGS) machines may contain adapter, linker, barcode and fingerprint sequences. TagDust2 is a program to extract and correctly label the sequences to be mapped in downstream pipelines. TagDust allows users to specify the expected architecture of a read and converts it into a hidden Markov model. The latter can assign sequences to a particular barcode (or index) even in the presence of sequencing errors.
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MutAid
MutAid: Sanger and NGS based pipeline for mutation screening.
MutAid: Sanger and NGS based integrated pipeline for mutation identification, validation and annotation in molecular diagnosis. MutAid is an integrated pipeline for mutation screening in clinical research. It can analyze Sanger sequencing and NGS data from raw reads to list of annotated mutation list. MutAid can analyze and interpret raw sequencing data produced by Sanger or several NGS sequencing platforms. -
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olego
OLego – short or long RNA-seq read mapping to discover exon junction
OLego is a program specifically designed for de novo spliced mapping of mRNA-seq reads. OLego adopts a seeding and extension scheme, and does not rely on a separate external mapper. It achieves high sensitivity of junction detection by using very small seeds (12-14 nt), efficiently mapped using Burrows-Wheeler transform (BWT) and FM-index. This also makes it particularly sensitive for discovering small exons. It is implemented in C++ with full support of multiple threading, to allow fast...
