miniasm: very fast OLC-based de novo assembler for noisy long reads
Miniasm is a very fast OLC-based de novo assembler for...nutes to assemble a bacterial genome. Under the default setting,...p;(only 40X are used, not the whole dataset), miniasm finishes the...accurate. In addition, on the whole data set (assembled in ~30 min...2411 days ago
Opera: An optimal genome scaffolding program
Opera (Optimal Paired-End Read Assembler) is a sequence assembly program (http://en.wi...th features for the assembly of large and complex genomes.Song Gao, Denis Bertrand, Bu...xact scaffolding of large, repeat-rich eukaryotic genomes with...2411 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.2411 days ago
simNGS and simLibrary – Software for Simulating Next-Gen Sequencing Data
simNGS is software for simulating observations from Illumina sequencing machines using the statistical models behind the AYB base-calling software. By default, observation...2410 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 has been postulated a...ble that we used for sequencing the S. cerevisiae genome. To make use of these data, w...re complete representation of the features of the genome and co...2409 days ago
Computational Genomics: Applied Comparative Genomics
The primary goal of the course is for students to be grounded in theory and leave the...antitative approaches for comparing and analyzing genomes starting from raw sequencing...across the tree of life. The topics will include genome assemb...2409 days ago
2409 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 clicking on "instructions" in each tab on the r...2409 days ago
Scripts for the analysis of HGT in genome sequence data.
Scripts for the analysis of HGT in genome sequence data2409 days ago
dnaPipeTE: de-novo assembly & annotation Pipeline for Transposable Elements
dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline desig...is very useful to quantify the proportion of TEs in newly sequenced genomes since it does not require genome assemb...2406 days ago