ONT assembly and Illumina polishing pipeline
This pipeline performs the following steps: Assembly of nanopore reads using Canu. Polish canu co...a paired-end Illumina dataset onto the contigs obtained in the previous steps using BWA mem. P...2419 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...cer. It includes a functions to generate a number plots for examining...is an emerging and rapidly developing technology. It is not clear what...smith@embl.de. If you’re not interested in the quality assement...2419 days ago
SIMA C++ Implementation: Simultaneous Multiple Alignment of LC/MS Peak Lists
...e package contains C++ source code as well as two binary files. The latter were tested under various operating s...nt of LC/MS Peak Lists, Bioinformatics 27(7):987-993. [doi] [techreport]2419 days ago
miniasm: very fast OLC-based de novo assembler for noisy long reads
...iniasm does not have a consensus step. It simply concatenates pieces of read sequences...data sets. Including the mapping step, it takes about 3 minutes to...ing reads overlapping, in ~10 minutes with 16 CPUs. The total asse...sample PacBio from the PBcR website wget -O- http://www.cbcb.umd...2415 days ago
RITA: Rapid identification of high-confidence taxonomic assignments for metagenomic data
...tify cases where both types of classifier are in agreement, which constitute the highest-confidence set. Sequences not classified in this manner are subjected to a series of downstream cl...2415 days ago
Opera: An optimal genome scaffolding program
...y order and orient contigs assembled from shotgun-sequencing reads.An updated version called OPERA-LG has...affolding of large, repeat-rich eukaryotic genomes with performance guarantees. Genome Biology, May 2016,...2415 days ago
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.2415 days ago
DRAWID: user-friendly Java software for chromosome measurements and idiogram drawing
"DRAWID has number of advantages including a user-friendly interactive interface, possibility for simultaneous chromosome and FISH/GISH/banding signal measurement and idiogram drawing as...2415 days ago
simNGS and simLibrary – Software for Simulating Next-Gen Sequencing Data
...base-calling software. By default, observations only incorporate noise due to sequencing and do not incorporate effects from more esoteric so...cles observed in an actual run of the machine, randomly generates noisy intensities representi...2414 days ago
Oxford Nanopore Sequencing, Hybrid Error Correction, and de novo Assembly of a Eukaryotic Genome
...olecules through a membrane pore has been postulated as a method for sequencing D...long read lengths (5-50kbp) at such high error rate (between ~5 and 40% error). W...ovo assembly that is highly contiguous and accurate: the contig N50 length is mor...2413 days ago