poRe: an R package for the visualization and analysis of nanopore sequencing data
Motivation: The Oxford Nanopore MinION device represents a u...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...2407 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’s MinION sequencer. It incl...interested in the quality assement of the raw or event level data, and want to jump straight to...2406 days ago
miniasm: very fast OLC-based de novo assembler for noisy long reads
Miniasm is a very fast OLC-based de nov...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...2403 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...2403 days ago
simNGS and simLibrary – Software for Simulating Next-Gen Sequencing Data
simNGS is software for simulating observations from Illumina sequencing machines using the s...orate effects from more esoteric sources of noise that may be present in real data ("dust", bubbles, merged clus...2402 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...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...2401 days ago
Computational Genomics: Applied Comparative Genomics
The primary goal of the course is for students to be grounded in theory and leave the course...e approaches for comparing and analyzing genomes starting from raw sequencing data. The course will focus on hum...2401 days ago
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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...2401 days ago
phyloXML: XML for evolutionary biology and comparative genomics
phyloXML (example) is an XML language designed to...be phylogenetic trees (or networks) and associated data. PhyloXML provides elements f...interoperability between various applications and databases. Furthermore, both due t...2401 days ago