Search Results for "snp"
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Showing 117 open source projects for "snp"
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somatic.sh
script for somatic SNP and Indel calling
somatic.sh is a shell script to run varscan somatic for somatic variant-calling, and Annovar to annotate. It calls both SNPs and Indels. It also produces 2 MAF files compatible with MutSigCV. Now the script allows for multithreading. The script is updated according to new format. -
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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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DSXR18
Aautomatically downloads snapshots from the Behringer XR18
...In the *.scn file, it saves the name of the snapshot in such a way that after loading the file, it is set in the Snapshots window so that the scene can be saved under its original name. *.scn files are compatible with the X-AIR-Edit program. https://www.buymeacoffee.com/piotrzaczek/dsxr18-kopiuje-snp-z-xr18 -
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ntx
Neutrality tests using the SNP site frequency spectrum
Tests on "neutrality" are designed to detect systematic deviations from chance patterns in genetic data. This tool computes for a given SNP site frequency spectrum some standard test statistics like Tajima's D, Fay & Wu's H, etc. Additionally, the user may adapt the tests to specific demographies by specifying non-standard first and secondary moments. These can be obtained e.g. from simulations. -
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A tool to estimate trends in recent effective population size trajectories using genome-wide SNP data.
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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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ParseCNV CNV call association software takes CNV calls as input and creates SNP based statistics for CNV occurrence in population study cases and controls then calls CNVRs based on neighboring SNPs of similar significance.
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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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variantkey
Binary files for variantkey
Binary files for the variantkey library: https://github.com/Genomicsplc/variantkey The binary files are generated using the script: https://github.com/Genomicsplc/variantkey/blob/master/resources/tools/vkhexbin.sh from the Human Variation Sets in VCF Format [National Library of Medicine (NLM)]: ftp://ftp.ncbi.nih.gov/snp/organisms/ -
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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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PPLine
SNP calling, annotation and gene/transcripts expression quantification
...PPLine provides: - read mapping (STAR/Tophat2/bowtie/bowtie2), including novel splice junsctions discovery - gene and transcript expression estimation (HTSeq-count/Cufflinks) - SNP calling with BQSR and indel realignment (samtools/GATK) - variant annotation (Annovar) - novel transcripts discovery (Cufflinks) - predicting proteotypic peptides and creating ref/alt proteins fasta-database - integration of the results -
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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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fcGENE: Genotype format converter
Format converting tool for genotype Data (e.g.PLINK-MACH,MACH-PLINK)
Main application is twofold: first to convert genotype SNP data into formats of different imputation tools like PLINK MACH, IMPUTE, BEAGLE and BIMBBAM, second to transform imputed data into different file formats like PLINK, HAPLOVIEW, EIGENSOFT and SNPTEST. Readable file formats: plink-pedigree (ped and map), plink-raw, plink-dosage, mach , minimac, impute, snptest, beagle and bimbam. -
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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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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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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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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. ...
