Latest paper on comparison of mapping tools
A. Hatem, D. Bozdag, A. E. Toland, U. V. Catalyurek "Benchmarking short sequence mapping tools" BMC Bioinformatics, 14(1):184, 2013. http://bmi.osu.edu/hpc/software/benchmark/ http://bmi.osu.edu/hpc/software/pmap/pmap.html Other similiar papers: http://online.liebertpub.com/doi/pdf/10.1089/cm...Tags: Sequencing, short reads mapping, SNP, GSNAP, BWA, Bowtie, BWA, mrsFAST
3900 days ago
Tags: Bioinformatics, SNP, SNPGenie, Perl
2596 days ago
Tags: kSNP3.0, SNP, detection, phylogenetic, analysis, genomes, alignment, reference, genome
2343 days ago
Tags: Heap, sensitive, accurate, SNP, detection, tool, low-coverage, high-throughput, sequencing, data
2212 days ago
Snippy: Rapid haploid variant calling and core SNP phylogeny
Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels). It will use as many CPUs as you can give it on a single computer (tested to 64 cores). It is designed with speed in mind, and produces a cons...Tags: Snippy, Rapid, haploid, variant, calling, core, SNP, phylogeny, bacteria
2029 days ago
Platypus: A Haplotype-Based Variant Caller For Next Generation Sequence Data
Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data. By using local realignment of reads and local assembly it achieves both high sensitivity and high specificity. Platypus can detect SNPs, MNPs, short indels, replacements and (using th...Tags: Platypus, Haplotype-Based, Variant, Caller, Next, Generation, Sequence, Data, NGS, SNP
2023 days ago
Π-cyc: A Reference-free SNP Discovery Application using Parallel Graph Search
Reference free SNP search for comparative population genomics: multiple samples run simultanously. **experimental phase, compiles and runs with OpenMPI-1.8.8 with Intel Compiler only Cycles enumeration (aka Bubbles) as part of de novo de bruijn graphs assembly using colours can be unpractical fo...Tags: Π-cyc, Reference-free, SNP, Discovery, Application, Parallel, Graph, Search
1563 days ago
Tags: RAINBOWR, Reliable, Association, INference, R, SNP, GWAS
1531 days ago
QuasiModo - Quasispecies Metric Determination on Omics
This repository contains the scripts and pipeline that reproduces the results of the HCMV benchmarking study. In this study we evaluated genome assemblers and variant callers on 10 in vitro generated, mixed strain HCMV sequence samples, each consisting of two lab strains in different abundance ra...Tags: QuasiModo, Quasispecies, Metric, Determination, Omics, Virus, Genome, Variant, Assembly, SNP
1048 days ago
DAVI: Deep learning-based tool for alignment and single nucleotide variant identification
DAVI consists of models for both global and local alignment and for variant calling. We have evaluated the performance of DAVI against existing state-of-the-art tool sets and found that its accuracy and performance is comparable to existing tools used for bench-marking. We further demonstrate tha...Tags: DAVI, deep, alignment, variant, identification, tool, snp
1150 days ago