miniasm: very fast OLC-based de novo assembler for noisy long reads
...) as input and outputs an assembly graph in the GFA format...tes pieces of read sequences to generate the final unitig ...embly (on Y). They are broadly comparable. Of course, the HGAP3 cons...mblies. Minimap and miniasm are ultrafast tools for (i) mapping and...2412 days ago
RITA: Rapid identification of high-confidence taxonomic assignments for metagenomic data
...ions from a Naive Bayes classifier, RITA is able to achieve very high accuracy on short reads. Unlike othe...has been accepted for publication: MacDonald NJ, Parks DH, and Beiko RG. Rapid identification of taxonomi...2412 days ago
Opera: An optimal genome scaffolding program
Opera (Optimal Paired-End Read Assem...er) is a sequence assembly program (http://en.wikipedia.org/wik...s.An updated version called OPERA-LG has been re-engineered wit...ex genomes.Song Gao, Denis Bertrand, Burton K. H. Chia and Nira...ttps://genomebiology.biomedcentral.com/articles/10.1186/s13059-...2412 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.2412 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 simultaneo...H/GISH/banding signal measurement and idiogram drawing as well as number of...in the scientists. "The output of the program is Microsoft XL table and pu...2412 days ago
simNGS and simLibrary – Software for Simulating Next-Gen Sequencing Data
...B base-calling software. By default, observations only incorporate noise due to sequencing and do not incorporate effects from more esoteric...en bases and cycles observed in an actual run of the machine, randomly generates noisy intensi...2411 days ago
Oxford Nanopore Sequencing, Hybrid Error Correction, and de novo Assembly of a Eukaryotic Genome
...ress of DNA molecules through a membrane pore has been postulated as...a method for sequencing DNA for several decades. Recently, a nanopor...engths (5-50kbp) at such high error rate (between ~5 and 40% error)....y that is highly contiguous and accurate: the contig N50 length is m...2410 days ago
Computational Genomics: Applied Comparative Genomics
...or comparing and analyzing genomes starting from raw sequencing data. The course...e topics will include genome assembly & comparative genomics, variant identif...quire familiarity with UNIX scripting and/or programming to complete the assignme...2410 days ago
2410 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 "inst...2410 days ago