ONT assembly and Illumina polishing pipeline
This pipeline performs the following steps: Assembly of nanopore reads using Canu. Polish canu contigs using racon (optional). Map a paired-end Illumina dataset onto th...2418 days ago
IONiseR: tools for the quality assessment of data produced by Oxford Nanopore’s MinION sequencer
...interested in the quality assement of the raw or event level data, and want to jump straight to the getting FASTQ format files from fast5 files you can go straight to the final sec...2418 days ago
SIMA C++ Implementation: Simultaneous Multiple Alignment of LC/MS Peak Lists
...s Vista 32bit, Windows 2008 Server, Windows 7 32bit and 64bit, Ubuntu 10.04 64bit, Ubuntu 10.10 64bit, and gentoo AMD64. The corresponding publication can be found here: B. Voss*, M....2417 days ago
miniasm: very fast OLC-based de novo assembler for noisy long reads
...all-vs-all read self-mappings (typically by minimap) as input...have a consensus step. It simply concatenates pieces of read sequenc...nbsp;ERS743109 and a deprecated PacBio E. coli data set. O...t also shows that minimap can be used as a read overlapper...2414 days ago
RITA: Rapid identification of high-confidence taxonomic assignments for metagenomic data
...from BLAST or UBLAST with compositional classifications from a Naive Bayes class...assified, RITA uses a pipeline to first identify cases where both types of classi...ion steps. This work has been accepted for publication: MacDonald NJ, Parks DH,...2414 days ago
Opera: An optimal genome scaffolding program
...orient contigs assembled from shotgun-sequencing reads.An updated version called OPERA-LG has been re-engi...Burton K. H. Chia and Niranjan Nagarajan. OPERA-LG: efficient and exact scaffolding of large, repeat-rich...2414 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.2414 days ago
simNGS and simLibrary – Software for Simulating Next-Gen Sequencing Data
...observations from Illumina sequencing machines using the statistical models behind the AYB base-calling software. By default, ob...ities representing the signals for the sequence at each cycle and calculates likelihoods for all p...2413 days ago
Oxford Nanopore Sequencing, Hybrid Error Correction, and de novo Assembly of a Eukaryotic Genome
...ted as a method for sequencing DNA for several decades. Recently, a nanopore-base...(https://github.com/jgurtowski/nanocorr) specifically for Oxford Nanopore reads,...tures of the genome and correctly assembles gene cassettes, rRNAs, transposable e...2412 days ago
Computational Genomics: Applied Comparative Genomics
...sequencing data. The course will focus on human genomics and human medical applications, but the techniques will...ased on assignments, a midterm exam, class presentations, and a significant class project. There are no...2412 days ago