INC-Seq: accurate single molecule reads using nanopore sequencing
INC-Seq reads enabled accurate species-level classification, identification of species at 0.1 % abundance and robust quantification of relative abundances, providing a cheap and effective approach for pathogen detection and microbiome profiling on the MinION system.2397 days ago
simNGS and simLibrary – Software for Simulating Next-Gen Sequencing Data
simNGS is software for simulating observations from Illumina sequencing machines using the statistical models behind the AYB base-cal...tware. By default, observations only incorporate noise due to sequencing and do not incorporate effect...2396 days ago
Oxford Nanopore Sequencing, Hybrid Error Correction, and de novo Assembly of a Eukaryotic Genome
Monitoring the progress of DNA molecules through a membrane pore has been postulated as a method for sequencing DNA for several decades. Recently, a nanopore-based sequencing instrument, the Oxford Nanopo...2395 days ago
Computational Genomics: Applied Comparative Genomics
The primary goal of the course is for students to be grounded in theory and leave the c...uantitative approaches for comparing and analyzing genomes starting from raw sequencing data. The course will focus o...2395 days ago
MetaSim A Sequencing Simulator for Genomics and Metagenomics.
Our software can be used to generate collections of synthetic reads that refl...t reads from the metagenome using a simulation of a number of different sequencing technologies. A population sa...2390 days ago
Musket: a multistage k-mer spectrum based corrector
Musket is a well-established leading next-generation sequencing read error correction algorithm targetting Illumina sequencing. This corrector employs the k-mer spectrum approach and introduces three correction tec...2388 days ago
SVfinder: Tool for detecting genomic rearrangement form DNA-seq data
SVfinder provides genome-wide detection of structural variants from next generation paired-end sequencing reads.2380 days ago
NanoSim: nanopore sequence read simulator based on statistical characterization.
NanoSim, a fast and scalable read simulator that captures the technology-specific fea...llows for adjustments upon improvement of nanopore sequencing...a set of read profiles serving as the input to the next step, the simulation stage. The sim...2376 days ago
dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes.
...ighly polymorphic (HP) diploid genomes remains challenging. As a result, there is a shortage of tools for assembling HP genomes from the next generation sequencing (NGS) data. The initial appro...2373 days ago
Meraculous: Haplotype-sensitive Assembly of Highly Heterozygous genomes.
Meraculous is a whole genome assembler for Next Generation Sequencing data geared for large genomes. It is a hybrid k-mer/read-based assembler that capitalizes on the high accuracy of Illumina...2373 days ago