Search Results for "snp"
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Showing 73 open source projects for "snp"
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proSeq
ProSeq is a GUI program to edit and analyse DNA polymorphism datasets
...It shows sequence alignments in a graphical window and allows the user to edit, manipulate and analyse sequences in various ways. ProSeq4 includes tools to analyse DNA polymorphism, scan for selection, do PCA and reconstruct phylogenies from sequence or SNP data. The program can also run coalescent simulations and generate and visualise phylogenies. The main changes in Proseq4 compared to Proseq3: - Multiplatform. Binaries available for Windows, Mac and Ubuntu. - It is now a 64-bit program, which can handle larger datasets (genome-scale from multiple individuals). - TreeViewer can show multiple phylogenies in densiTree-like style - Principal components analysis Disclamer: No warranty of any kind is provided - use at your own risk -
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kSNP
kSNP4 does SNP discovery and SNP annotation from whole genomes
kSNP4 identifies the pan-genome SNPs in a set of genome sequences, and estimates phylogenetic trees based upon those SNPs. SNP discovery is based on k-mer analysis, and requires no multiple sequence alignment or the selection of a reference genome, so kSNP4 can take 100's of microbial genomes as input. A SNP locus is defined by an oligo of length k surrounding a central SNP allele. kSNP4 can analyze both complete (finished) genomes and unfinished genomes in assembled contigs or raw, unassembled reads. ... -
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PhaseDel
Phasing-based somatic deletion caller from single-cell WGS data
...It is highly specialized for discriminating genuine somatic focal deletions (several bases to kilo-bases in length) from excessive SV-like artifacts, which are inevitably occurring during single-cell whole-genome amplification. PhaseDel accurately detects such true deletions based on the linkage information between deletion breakpoints and nearby germline heterozygous SNP sites. The important features of PhaseDel are: • Accurate identification of somatic focal deletions at single-base-pair resolution in scWGS using phasing information • Estimation of the genome-wide somatic deletion rate for a given cell with the controlled FDR level • Characterization of underlying DSB repair mechanisms for identified deletion candidates A more detailed description of the tool is provided in the [[wiki]] tab. -
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gsasnp2
PubMed ID: 29562348 / DOI: 10.1093/nar/gky175
* GSA-SNP2 is a successor of GSA-SNP (Nam et al. 2010, NAR web server issue). GSA-SNP2 accepts human GWAS summary data (rs numbers, p-values) or gene-wise p-values and outputs pathway genesets ‘enriched’ with genes associated with the given phenotype. It also provides both local and global protein interaction networks in the associated pathways. * Article: SYoon, HCTNguyen, YJYoo, JKim, BBaik, SKim, JKim, SKim, DNam, "Efficient pathway enrichment and network analysis of GWAS summary data using GSA-SNP2", Nucleic Acids Research, Vol. 46(10), e60(2018)... -
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MetaPhat -meta-pheno-association-tracker
Multivariate traits genome-wide association analysis and decomposition
MetaPhat is an open sourced program to detect optimal subset traits on lead SNP associations from multiple biomarker GWAS summary results. Best traits are derived from systematic decomposing multivariate associations into central traits based on optimal BIC and P-value from multivariate CCA models. SNP trace results are plotted and clustered to dissect and improve the specificity of mv phenotype-genotype associations. -
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snpEff is a fast variant effect predictor (SNP, MNP and InDels) for genomic data. It is integrated with Galaxy so it can be used either as a command line or as a web application.
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MIRA V5 is available only on GitHub! The V4 version released here on SourceForge stay up as some automated release fetching packages rely on V4. MIRA - Sequence assembler and sequence mapping for whole genome shotgun and EST / RNASeq sequencing data. Can use Sanger, 454, Illumina and IonTorrent data. PacBio: CCS and error corrected data usable, uncorrected not yet.
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hppRNA
A Snakemake-based handy parameter-free pipeline for RNA-Seq analysis
hppRNA package is dedicated to the RNA-Seq analysis for a large number of samples simultaneously from the very beginning to the very end, which is formulated in Snakemake pipeline management system. It starts from fastq files and will produce gene/isoform expression matrix, differentially-expressed-genes, sample clusters as well as detection of SNP and fusion genes by combination of the state-of-the-art software. The first version handles protein-coding genes, lncRNAs and circRNAs and includes six core-workflows such as (1) Tophat - Cufflink - Cuffdiff; (2) Subread - featureCounts - DESeq2; (3) STAR - RSEM - EBSeq; (4) Bowtie - eXpress - edgeR; (5) kallisto - sleuth; (6) HISAT - StringTie - Ballgown. ... -
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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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FEATnotator is a light weight, fast and easy to use, open source software program that annotates different kinds of next generation analysis data based on known reference genome annotation information. For SNP data, it also predicts the effect of SNPs in the protein coding regions on the codons involved and marks SNPs potentially affecting start and stop codons and splice sites. It also identifies features of user’s interest, such as genes, or biomarkers in the vicinity of the features to be annotated. The output also includes tables and graphs summarizing the distribution of the annotated features.
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BisSNP
Bisulfite-seq/NOMe-seq SNPs & cytosine methylation caller
...It works for both of single-end and paired-end reads.Specificity and sensitivity has been validate by Illumina IM SNP array. In default threshold 30X data (Phred scale score > 20), it could detect 92.21% heterozygous SNPs with 0.14% false positive rate Cytosine calling is not only based on reference context, so it could detect non-reference cytosine context. Google group for help: http://goo.gl/zL7Nj -
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A comparative synteny analysis tool for target-gene SNP marker discovery: connecting genomics data to breeding in Solanaceae * The foundation of this web source is CodeIgniter. * After setting the CodeIgniter framework, unzip it under the default home directory. The database is based on Maria DB (mysql). Download the schema and import it into the DB. Each species you want to analyze needs blast results.
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REHUNT
REHUNT (Restriction Enzymes HUNTing)
REHUNT (Restriction Enzymes HUNTing) is a free and open source package implemented in JAVA for providing many useful methods for biological sequence analysis (especially in SNP genotyping) around restriction enzymes. All academic researchers are encouraged to use REHUNT in their studies or to integrate it into their systems and applications. Non-academic users or commercial needs are also welcome to use it. For further information or additional applications, please contact the author Yu-Huei Cheng <yuhuei.cheng@gmail.com>. -
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GPU3SNP
Exhaustive search for third order epistatic interactions using CUDA
GPU3SNP is a multi-GPU tool that exhaustively analyzes case-control datasets looking for 3-SNP combinations that present epistatic interaction. It provides a list with the combinations that have higher Mutual Information, which is used as measure for interaction. It is parallelized using CUDA and can exploit several GPUs in the same node/system. -
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Edesign
Primer and enhanced internal probe design tool
... - Functions for designing internal probes are greatly enhanced. - "Genotyping mode" provides design of the internal probe over a user-specified target variant e.g. (SNP, insert/deletion, somatic mutation etc) for genotyping. - Modified oligonucleotide can be designed. The original Edesign treats Eprobe and Eprimer. For technical support please contact: contact@dnaform.jp -
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6. DHOEM (Windows)
R function which incorporates simulated markers to a real data set
DHOEM (Densification of Haplotypes by lOEess and Maximum Likelihood) is a novel R application which performs simulation of new markers in real SNP marker data. The new markers are generated according to real local data characteristics, modeled statistically, and are interpolated locally between real markers in the data. The function allows the user to specify a desired level of marker density, with a minor allele frequency (MAF) limit, which is produced in a reasonable computation time. ... -
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5.Kernelized qtl-haplotype mapping (HPC)
Fortran/R program for kernelized qtl-haplotype mapping by mixed model
Kernelized qtl-haplotype mapping (named KHAMMIX) is a Fortran/R program which performs parallel haplotype based scans of chromosomes, by mixed model analyses, for diploid organisms. Two kernels; the Gaussian and Van Raden kernels, are allowed for the mixed model analyses. The haplotypes are defined by a sliding window of L SNP markers (L is an integer greater or equal to 1). Hence, 2^L haplotypes can be (not necessarily) observed for a sliding window (e.g. 2^6=64 for L=6). Reference: http://gsejournal.biomedcentral.com/articles/10.1186/1297-9686-46-45 -
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SPRITE
Parallel SNP detection pipeline
SPRITE is an open-source software package providing a parallel implementation of the Single Nucleotide Polymorphisms (SNP) detection genomic data analysis workflow. It consists of three tools: PRUNE for read alignment, SAMPA for intermediate file processing, and PARSNIP for parallel SNP calling. -
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OPTPDT
OPTPDT is a family-based multi-SNP association test
OPTPDT is a family-based multi-SNP association test. A variable p-value threshold algorithm is used in the test to select an optimal subset of SNPs that has the strongest association signals. -
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GOBIG is a toolbox that can be used for detecting genetic variations. The project is intended to handle big data. What's more important is that it be used to detect clusters of SNP variants. It is the intention to use the toolbox with common and rare variants. To use it, for example, to find the genetic map of genes causing complex diseases.
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Auto Primer3
Automatically design primers to genes/coordinates using primer3.
PLEASE NOTE: THIS PROJECT PAGE WILL NO LONGER BE UPDATED - PLEASE USE THE GITHUB PAGE (https://github.com/gantzgraf/autoprimer3) TO FIND THE LATEST RELEASE (https://github.com/gantzgraf/autoprimer3/releases/latest). AutoPrimer3 retrieves gene information, DNA sequences and SNP information from the UCSC genome browser and uses primer3 to automatically design primers to genes or genomic coordinate targets. Primers may be designed using information from any of the UCSC hosted genomes and primers can be made to avoid overlapping SNPs for genomes where SNP databases are available. -
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gametes
Generate complex SNP models and heterogeneous datasets
...Version 2.0, adds the ability to generate heterogeneous datasets by applying multiple independent models to different subsets of the simulated data. Additionally we have added a custom model generation feature, so that users may directly specify and examine the properties of any 2 or 3 locus SNP model. Simple Mendelian models may also be generated with this feature. -
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SNiPlay is a web-based pipeline and database for SNP analysis and management
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coval
Improving the quality of short read alignment data
Coval is designed to minimize the incidence of spurious alignment of short reads, by filtering mismatched reads that remained in alignments after local realignment and error correction of mismatched reads, thereby increasing the calling accuracy of currently available tools for SNP and indel identification. -
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CCH
A genetics tool that identifies genomic regions of shared ancestry
Combinatorial Conflicting Homozygosity (CCH) uses dense Single Nucleotide Polymorphism (SNP) genotypes to identify regions of the genome inherited from a common ancestor among any or all subsets of a group. Analysis is rapid and can identify loci containing genes for dominant traits. CCH is robust to the presence of phenocopies and can detect undisclosed shared common ancestry. The associated publication regarding CCH may be accessed here: http://www.biomedcentral.com/1471-2164/16/163 If you use CCH please cite: Levine AP, Connor TM, Oygar DD, Neild GH, Segal AW, Maxwell PH, Gale DP. ...
