poRe: an R package for the visualization and analysis of nanopore sequencing data
Motivation: The Oxford Nanopore MinION device represents...and build a suite of tools specifically for MinION data. Results: Here we prese...summarize and visualize MinION nanopore sequencing data. As a package for R, poRe has...2418 days ago
IONiseR: tools for the quality assessment of data produced by Oxford Nanopore’s MinION sequencer
This package is intended to provide tools for the quality assessment of data produced by Oxford Nanopore&r...in the quality assement of the raw or event level data, and want to jump straight to...2418 days ago
miniasm: very fast OLC-based de novo assembler for noisy long reads
Miniasm is a very fast OLC-based de...ford Nanopore (ONT) bacterial data sets. Including the mapping s...assembles 9 out of 12 PacBio datasets and 3 out of 4 ONT datase...te. In addition, on the whole data set (assembled in ~30 min), t...| tar zxf - ln -s selfSampleData/pacbio_filtered.fastq reads.f...2415 days ago
RITA: Rapid identification of high-confidence taxonomic assignments for metagenomic data
RITA is a standalone software package and Web server for taxonomic assignment of metagenomic sequence reads. By combining homology predictions from BLAST or UBLAST wit...2415 days ago
simNGS and simLibrary – Software for Simulating Next-Gen Sequencing Data
simNGS is software for simulating observations from Illumina sequencing machines using th...orate effects from more esoteric sources of noise that may be present in real data ("dust", bubbles, merged clus...2414 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 po...ing the S. cerevisiae genome. To make use of these data, we developed a novel open-so...on of the nanopore reads using complementary MiSeq data and produce a de novo assembl...2413 days ago
Computational Genomics: Applied Comparative Genomics
The primary goal of the course is for students to be grounded in theory and leave the cou...e approaches for comparing and analyzing genomes starting from raw sequencing data. The course will focus on hum...2413 days ago
2413 days ago
Ribbon: Visualizing complex genome alignments and structural variation:
Ribbon can be used for long reads, short reads, paired-end reads, and assembly/genome alignments. Instructions for each data format are available by click...2413 days ago
phyloXML: XML for evolutionary biology and comparative genomics
phyloXML (example) is an XML language designed...be phylogenetic trees (or networks) and associated data. PhyloXML provides elements f...interoperability between various applications and databases. Furthermore, both due t...2412 days ago