Search Results for "ngs"
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Showing 145 open source projects for "ngs"
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popoolation
estimate natural variation and positive selection
...One of the main challenges in population genomics is to identify regions of intererest on a genome wide scale. We believe that PoPoolation will greatly aid this task by allowing a fast and user friendly analysis of NGS data from DNA pools. Documentation: https://sourceforge.net/p/popoolation/wiki/Main/ -
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MicroRNAs (miRNAs) are of significance in tuning and buffering gene expression. Despite abundant analysis tools have been developed in the last two decades, plant miRNA identification from next-generation sequencing (NGS) data remains challenging. Here present a user-friendly pure Java-based software package, SRICATs, which enable researchers to perform all steps of plant miRNA analysis based on convolutional neural network methods. SRICATs outperforms currently popular software tools on the test data from five plant species: Oryza sativa, Arabidopsis thaliana, Sorghum bicolor, Chlamydomonas reinhardtii and Physcomitrella patens.
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MiModD
Mutation Identification in Model Organism Genomes using Desktop PCs
MiModD is a software package for genomic variant identification from next-generation sequencing (NGS) data with optimized usage of system resources and a user-friendly interface. For most model organism genomes it lets the user carry out a complete analysis from unaligned genomic NGS read data to an annotated list of variants on a regular Desktop PC within a few hours. Its user-interface is beginner-friendly and designed to encourage geneticists to analyze NGS data themselves without the help of a trained bioinformatician. -
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MutaNET
NGS Pipeline and Automated Mutation Analysis
MutaNET comes with a next generation sequencing (NGS) pipeline that calls mutations based on paired-end NGS reads, an automated mutation analysis tool and various file converters and mergers. The mutation analysis feature considers the coding region, protein domains, regulation and transcription factor binding site information, and can be used to analyse the potential impact of mutations on antibiotic resistance. -
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miRDP2
Accurately and fast analyzing microRNAs transcriptome in plants
...We have tested miRDP2 to analyze miRNA transcriptomes in such plants with gradually increased genome size as Arabidopsis, rice, tomato, maize and wheat. Compared with miRDeep-P and several other computational tools, miRDP2 processed NGS data with superior speed. By incorporating newly updated plant miRNA annotation criteria, the accuracy of miRDP2 is also markedly improved. Our results demonstrate miRDP2 as a fast and accurate tool for analyzing the miRNA transcriptome in plants. Reference: https://doi.org/10.1093/bioinformatics/bty972 -
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dnaasm
set of tools for NGS data analysis
genome de novo assembler for next generation sequencing data, tool to link contigs by long DNA reads -
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AGELESS
Software for systematic study of Parents and their hybrids
NGS technology although has its obvious advantages, poses serious bioinformatics challenges in analyzing and extracting meaningful information. Plenty of tools have been developed for the analysis of NGS data that are mostly catered towards diploid genomes. Despite such a rich tool set, it is difficult to improvise and use them on genomes which are aneuploid. -
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MToolBox
A bioinformatics pipeline to analyze mtDNA from NGS data
MToolBox is a highly automated bioinformatics pipeline to reconstruct and analyze human mitochondrial DNA from high throughput sequencing data. MToolBox includes an updated computational strategy to assemble mitochondrial genomes from Whole Exome and/or Genome Sequencing (PMID: 22669646) and an improved fragment-classify tool (PMID:22139932) for haplogroup assignment, functional and prioritization analysis of mitochondrial variants. MToolBox provides pathogenicity scores, profiles of genome... -
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FusionCatcher
Somatic fusion-genes finder for RNA-seq data
FusionCatcher searches for novel/known somatic fusion genes, translocations, and chimeras in RNA-seq data (paired-end reads from Illumina NGS platforms like Solexa and HiSeq) from diseased samples. The aims of FusionCatcher are: - very good detection rate for finding candidate fusion genes, - very easy to use (i.e. no a priori knowledge of databases and bioinformatics is needed in order to run FusionCatcher), - very good detection of challenging fusion genes, like for example IGH fusions, CIC fusions, DUX4 fusions, CRLF2 fusions, TCF3 fusions, etc... -
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vipie
http://vipie.rd.tuni.fi/vipie/index.html
...Vipie: web pipeline for parallel characterization of viral populations from multiple NGS samples. BMC Genomics 18, 378 (2017). https://doi.org/10.1186/s12864-017-3721-7 -
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CusVarDB
CusVarDB generated variant protein database from NGS-datasets
CusVarDB is a windows based tool for creating a variant protein database from Next-generation sequencing datasets. The program supports variant calling for Genome, RNA-Seq and ExomeSeq datasets. The program performs mainly 4 modules 1. Align the datasets with reference database 2. Perform the variant calling using Genome Analysis Toolkit (GATK) 3. Annotate the variant using ANNOVAR 4. Create the variant protein database Apart from the main modules, the program also supports... -
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FamPipe
A NGS analysis pipeline for families
FamPipe is a comprehensive analysis pipeline for family data. -
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FHiTINGS
Fungal High-throughput Taxonomic Identification tool for use with NGS
FHiTINGS is designed for use in rapidly identifying, classifying, and parsing internal transcribed spacer (ITS) DNA sequences after a BLASTn search. This software is useful for fungal ecology studies using next generation sequencing (NGS). See our paper in the Journal of Basic Microbiology (http://onlinelibrary.wiley.com/doi/10.1002/jobm.201200507/pdf) for more information and please cite that paper if you use our program. Thank you for using FHiTINGS! Note: FHiTINGS version 1-4 has been released. This uses an update to the BLAST database used by FHiTINGS. Also note that FHiTINGS must run on Python 2.4-2.7.1 (it will NOT run on Python 3.0 or higher)... -
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unitas
Complete annotation of small RNA datasets from NGS
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reditools
RNA editing detection by NGS data
...A-to-I substitutions may have profound functional consequences and have been linked to a variety of human diseases including neurological and neurodegenerative disorders or cancer. NGS technologies offer a unique opportunity to investigate RNA editing. REDItools are simple python scripts conceived to investigate RNA editing at large-scale. REDItools are now hosted at https://github.com/BioinfoUNIBA/REDItools -
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Phusion2
The genome assembly pipeline based on read clustering
Phusion2 is a pipeline for de novo genome assembly using NGS data. It is based upon a strategy called read clustering. Starting with kmer frequency analysis, this allows for a reasonable selection of the kmer sizes. K-tuples from raw reads are merged and sorted into a table so that multiple occurring kmer words shared by different reads can be linked. A relation matrix is used to record the shared kmer words among all the reads. -
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ART-DeCo
ART-DeCo uses polymorphism allelic ratio to predict contaminations
...ART-DeCo can be implemented in any NGS workflow, from gene panel to genome-wide analyses. Any polymorphism is helpfull. Rare SNPs and SNPs in linkage disequilibrium should be taken into account to consolidate predicted contaminations. -
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A genome wide mapping data interpretation platform for NGS(ChIPSeq). A tutorial can be found at: http://genomeast.igbmc.fr/wiki/doku.php?id=training:seqminer
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inGAP-family provides an efficient and effective framework to discover, filter and visualize DNA polymorphisms and structural variants from alignment of short reads. Applying this method on polymorphism detection on real datasets shows that elimination of artificial variants greatly facilitates the precise identification of meiotic recombination points, recognizing causal mutations in mutant genomes or QTL loci. In addition, inGAP-family provides user-friendly graphical interface for...
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PhageTerm
Determining Bacteriophage Termini and Packaging using NGS data.
NEW VERSION (PhageTermVirome) AVAILABLE AT : (To access the lightest version) https://gitlab.pasteur.fr/vlegrand/ptv/-/releases This new version is now compatible with PYTHON3 and now allows the analysis of multiple phage genomes/contigs (multifasta) in a single analysis. However, like before, you can still perform the analysis on a single phage genome/contig. Description : PhageTerm and PhageTermVirome are a theoretical and statistical framework to analyze DNA termini and... -
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CoVaMa
Co-Variation Mapper
CoVaMa (Co-Variation Mapper) (python) detects correlated patterns of mutations in a viral quasi-species. CoVaMa takes NGS alignment data (SAM) and populates large matrices of contingency tables that correspond to every possible pairwise interaction of nucleotides or amino acids in the viral genome. These tables are then analysed for evidence linkage disequilibrium. CoVaMa requires python version 2.7 and Numpy. -
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Meraculous-2D
Eukaryotic Genome Assembler
---------------------------------------- IMPORTANT: Meraculous-2D has been superseded by the HipMer assembler, available here: https://sourceforge.net/projects/hipmer/ ----------------------------------------- Meraculous-2D is a whole genome assembler for NGS reads (Illumina) that is capable of assembling large, diploid genomes with modest computational requirements. Features include: - Efficient k-mer counting and deBruijn graph traversal - Two modes of handling of diploid allelic variation - Improved scaffolding that produces more complete assemblies without compromising scaffolding accuracy. ...
