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  • SNP-Pipeline
    |{{#vardefine:app|snp-pipeline}} |{{#vardefine:url|https://github.com/CFSAN-Biostatistics/snp-pipeline}}
    3 KB (306 words) - 17:00, 10 June 2022
  • SNP-sites
    |{{#vardefine:app|snp-sites}} |{{#vardefine:url|https://github.com/sanger-pathogens/snp-sites}}
    3 KB (334 words) - 12:56, 15 August 2022

Page text matches

  • SNP-Pipeline
    |{{#vardefine:app|snp-pipeline}} |{{#vardefine:url|https://github.com/CFSAN-Biostatistics/snp-pipeline}}
    3 KB (306 words) - 17:00, 10 June 2022
  • SNPhylo
    ...peline, user can construct a phylogenetic tree from a file containing huge SNP data. ...H. (2014). SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data. BMC Genomics, 15(1).
    3 KB (340 words) - 17:48, 10 June 2022
  • SNP-sites
    |{{#vardefine:app|snp-sites}} |{{#vardefine:url|https://github.com/sanger-pathogens/snp-sites}}
    3 KB (334 words) - 12:56, 15 August 2022
  • Ksnp
    Gardner, S.N., T. Slezak, and B.G. Hall. 2015. kSNP3.0: SNP detection and kSNP v2 software for alignment-free SNP discovery and phylogenetics of hundreds
    3 KB (327 words) - 12:56, 15 August 2022
  • PennCNV
    ...appropriate preparation of file format, it can also handle other types of SNP arrays and oligonucleotide arrays. ...amples. It differs form segmentation-based algorithm in that it considered SNP allelic ratio distribution as well as other factors, in addition to signal
    4 KB (474 words) - 21:23, 6 December 2019
  • GSNP
    ...ucleotide polymorphism (SNP) is the most common form of genetic variation. SNP detection is to find a new polymorphism site and the known polymorphism all ...data and errors of alignment and experiment to use a Bayesian model based SNP detection algorithm for calculation of quality score of each base. These qu
    3 KB (459 words) - 17:27, 15 August 2022
  • SNPsplit
    ...SAM/ BAM format and determine the allelic origin of reads that cover known SNP positions. ...Psplit: Allele-specific splitting of alignments between genomes with known SNP genotypes]
    2 KB (282 words) - 20:38, 27 May 2022
  • FastStructure
    A variational framework for inferring population structure from SNP genotype data. ...ard. fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets , (Genetics) June 2014 197:573-589 ([http://rajanil.github.io/fas
    3 KB (297 words) - 18:54, 12 August 2022
  • GATK
    ...things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and a local realigner. ...evelopment library that underlies tools for common analysis problems (like SNP calling) as well as enabling exploratory research on NGS data.
    4 KB (540 words) - 16:53, 15 August 2022
  • SNPGenie
    ...and can be combined with upstream applications such as maximum-likelihood SNP calling techniques (e.g., see Lynch et al. 2014). For additional background
    3 KB (423 words) - 18:41, 1 June 2022
  • Fastsimcoal
    Different markers, such as DNA sequences, SNP, STR (microsatellite) or multi-locus allelic data can be generated under a ...sa, V.C., and M. Foll (2013) Robust demographic inference from genomic and SNP data. PLOS Genetics, 9(10):e1003905.]
    4 KB (481 words) - 15:25, 15 August 2022
  • Snippy
    Rapid haploid variant calling and core SNP phylogeny
    2 KB (237 words) - 14:37, 10 June 2022
  • SNAPE-pooled
    ...s probability is high enough, then you have a segregating position, a.k.a. SNP.
    2 KB (270 words) - 12:56, 15 August 2022
  • FGTPartitioner
    ...er: Parsimonious delimitation of ancestry breakpoints in large genome-wide SNP datasets. Journal of Open Source Software, 5(46), 2030, https://doi.org/10.
    2 KB (266 words) - 19:05, 28 June 2023
  • MAGMA-GWAS
    ...data. It can be used to analyse both raw genotype data as well as summary SNP p-values from a previous GWAS or meta-analysis.
    2 KB (273 words) - 19:35, 23 February 2021
  • PhaME
    ...haME extracts SNPs from complete genomes, draft genomes and/or reads. Uses SNP multiple sequence alignment to construct a phylogenetic tree. Provides evol
    2 KB (287 words) - 14:18, 9 March 2020
  • BOLT-LMM
    ...OLT-REML algorithm for variance components analysis (i.e., partitioning of SNP-heritability and estimation of genetic correlations).
    2 KB (289 words) - 16:24, 2 January 2020
  • RAiSD
    ...previously released tools (SweeD and OmegaPlus), RAiSD scans whole-genome SNP data based on a composite evaluation scheme that captures multiple sweep si
    2 KB (292 words) - 17:38, 14 July 2020
  • HapCompass
    ...d by the sequencing reads and viewed as supporting evidence of co-occuring SNP alleles in a haplotype.
    2 KB (287 words) - 18:13, 15 August 2022
  • Parsnp
    ...p is a command-line-tool for efficient microbial core genome alignment and SNP detection. Parsnp was designed to work in tandem with Gingr, a flexible pla
    3 KB (297 words) - 21:22, 6 December 2019
  • Quantisnp
    ...dden-Markov Model to detect and accurately map copy number variation using SNP genotyping data. Nucleic Acids Research, 35(6):2013-2025 2007.]
    2 KB (297 words) - 20:29, 12 August 2022
  • KING
    KING is a toolset making use of high-throughput SNP data typically seen in a genome-wide association study (GWAS) or a sequenci
    3 KB (305 words) - 19:28, 12 August 2022
  • NextGenMap
    ...of runtime. This allows analyzing large-scale datasets even with increased SNP rates or higher error rates (e.g. caused by specialized experimental protoc
    3 KB (309 words) - 16:24, 19 August 2022
  • FreeBayes
    ...predecessors (PolyBayes, GigaBayes, and BamBayes), it expands the scope of SNP and small-indel variant calling to populations of individuals with heteroge
    2 KB (302 words) - 18:55, 12 August 2022
  • Wgsim
    One can evaluate the accuracy of a mapper or a SNP caller with wgsim_eval.pl
    3 KB (343 words) - 21:29, 6 December 2019
  • SOLAR
    ...nents analysis, including linkage analysis, quantitative genetic analysis, SNP association analysis (QTN and QTLD), and covariate screening. Operations ar
    3 KB (328 words) - 21:24, 6 December 2019
  • FcGENE
    ...ata such as PLINK and MACH. The usage is two-fold. First, convert genotype SNP data into formats of different imputation tools like PLINK MACH, IMPUTE, BE
    3 KB (326 words) - 16:38, 15 August 2022
  • PolyGembler
    ...sumes availability of genome-wide genotyping data such as GBS, RAD-seq and SNP array data, collected on a F1 outbred mapping population, as well as high c
    3 KB (344 words) - 13:45, 3 November 2020
  • Dadi
    ...he joint demographic history of multiple populations from multidimensional SNP data" PLoS Genetics 5:e1000695 (2009).
    3 KB (350 words) - 21:21, 6 December 2019
  • RGI
    ...predict resistome(s) from protein or nucleotide data based on homology and SNP models. The application uses reference data from the Comprehensive Antibiot
    3 KB (352 words) - 21:24, 6 December 2019
  • Ngstools
    ...ical uncertainty. The methods implemented in these programs do not rely on SNP or genotype calling, and are particularly suitable for low sequencing depth * SNP calling, genotype calling, and sample allele frequency estimation from New-
    5 KB (708 words) - 15:31, 14 December 2022
  • Nanocaller
    ...aller uses long-range haplotype structure to generate predictions for each SNP candidate variant site by considering pileup information of other candidate
    3 KB (351 words) - 15:41, 16 March 2023
  • ADMIXTURE
    ...for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calc
    3 KB (366 words) - 20:51, 11 August 2022
  • Samtools
    Bcftools does the SNP calling. It can also concatenate BCF files, index BCFs for fast random acce
    3 KB (357 words) - 22:04, 21 August 2022
  • Deepvariant
    A universal SNP and small-indel variant caller using deep neural networks. Nature Biotechno
    3 KB (356 words) - 13:17, 16 April 2024
  • PGDSpider
    ...ograms for a vast range of data types (e.g. DNA, RNA, NGS, microsatellite, SNP, RFLP, AFLP, multi-allelic data, allele frequency or genetic distances). Be
    3 KB (387 words) - 19:04, 10 June 2022
  • SMR
    ...hodology can be interpreted as an analysis to test if the effect size of a SNP on the phenotype is mediated by gene expression. This tool can therefore be
    3 KB (362 words) - 18:27, 19 August 2021
  • ProbABEL
    ProbABEL software package is used for the analysis of genome-wide imputed SNP data and quantitative, binary, and time-till-event outcomes under linear, l
    3 KB (371 words) - 19:35, 21 August 2022
  • SHEsisPlus
    ...nbach U, Gebhardt C, Selbig J, Kersten B.Haplotype inference from unphased SNP data in heterozygous polyploids based on SAT. BMC Genomics 2008 Jul 30;9:35
    3 KB (344 words) - 15:04, 19 August 2022
  • Snp2hla
    ...med/24698974 Pillai NE et al. "Predicting HLA alleles from high-resolution SNP data in three Southeast Asian populations." Hum Mol Genet, [epub ahead of p
    3 KB (379 words) - 20:42, 12 August 2022
  • BamBam
    ;InterSnp: takes 1 or more BAM files and writes out a ".snp" file with a summary of all polymorphic loci
    3 KB (456 words) - 18:00, 12 August 2022
  • ART
    ...tion sequencing data analysis, including read alignment, de novo assembly, SNP and structure variation discovery. ART was used as a primary tool for the s
    3 KB (440 words) - 21:10, 6 December 2019
  • Gmap
    Fast and SNP-tolerant detection of complex variants and splicing in short reads
    3 KB (450 words) - 17:11, 15 August 2022
  • Phyluce
    * Alignment and SNP calling using UCE or other types of raw-read data.
    4 KB (517 words) - 18:23, 21 August 2022
  • SHAPEIT4
    ...a fast and accurate method for estimation of haplotypes (aka phasing) for SNP array and high coverage sequencing data. The version 4 is a refactored and
    5 KB (617 words) - 19:22, 14 December 2022
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