1440 days ago
NanoSim: nanopore sequence read simulator based on statistical characterization.
NanoSim, a fast and scalable read simulator that captures the technology-specific features of ONT data and allows for adjustments up...ion, which provides a comprehensive alignment-based analysis and generates a set of read p...2387 days ago
Delta: a new Web-based 3D genome visualization and analysis platform
Delta is an integrative visualization and analysis platform to facilitate visually annotating and exploring the 3D physical architecture of genomes. Delta takes Hi-C or ChIA-PET...2385 days ago
dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes.
While the number of sequenced diploid genomes have been steadily increasing in the l...ng HP genomes from the next generation sequencing (NGS) data. The initial approaches to assembling HP genomes were proposed in the pre-NGS era...2384 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-m...aculous achieves high performance with large datasets by utilizing lightweight...riety of architectures. https://jgi.doe.gov/data-and...2384 days ago
AIRVF: a filtering toolbox for precise variant calling in Ion Torrent sequencing
AIRVF that works on flowgram, raw and mapped reads and called variants to reduce artifact-driven false variant calls. Tests on sequencing data of...2383 days ago
Japanese Multi Omics Reference Panel, jMorp
Japanese Multi Omics Reference Panel, jMorp, is a database of metabolome and proteome data in plasma obtained from volunteers in ToMMo. Metabolome data were measured by proton NMR and LC-MS, and proteome data were obtained by n...2382 days ago
MeDuSa: a multi-draft based scaffolder
MeDuSa (Multi-Draft based Scaffolder), an algorithm for genome scaffolding. MeD...caffolders, it does not require either prior knowledge on the microrganisms dataset under analysis (e.g. their phylogenetic rela...2329 days ago
PASA: Gene Structure Annotation and Analysis
PASA, acronym for Program to Assemble Spliced Alignments, is a eukaryotic genome annotation tool that exploits sp...e annotation consistent with the most recently available experimental sequence data. PA...2378 days ago
snakepipes: A toolkit based on snakemake and python for analysis of NGS data
snakePipes are flexible and powerful workflows built using snakemake that simplify the analysis of NGS data. DNA-mapping* ChIP-seq* RNA-seq* ATAC-seq* scRNA-seq Hi-C Whole G...1859 days ago