CABOG: Celera Assembler with Best Overlap Graph
CABOG (Celera Assembler with Best Overlap Graph) is scientific software for DNA research. CABOG has been a critical component of many genome sequencing projects. CAB...2547 days ago
GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies.
GRASS (GeneRic ASsembly Scaffolder)-a novel algorithm for scaffolding second-generation sequencing assemblies capable of using diverse information sources. GRASS offers a...2539 days ago
AVID: A Global Alignment Program
A new global alignment method called AVID. The method is designed to be fast, memory efficient, and practical for sequence alignments of large genomic regions up to megab...2538 days ago
Grinder / Biogrinder - A versatile omics shotgun and amplicon sequencing read simulator
...versity. Grinder may also be used to help decide between alternative sequencing methods for a sequence-based project, e.g. should the library be paired-end or not, how many reads should...2538 days ago
NovelSeq: Novel Sequence Insertion Detection
The NovelSeq framework is designed to detect novel sequence insertions using high throughput paired-end whole genome sequencing data. http://novelseq.sourceforge.net/Home Paper at https://www.ncbi.nlm.nih.gov/pubmed/203857262522 days ago
orthodotter: Synteny plots (oxford grid)
orthodotter -h -------------------------------------------------------------------------------- orthodotter - Plot orthologous genes on an oxford grid. -f <f...2461 days ago
Meraculous: De Novo Genome Assembly with Short Paired-End Reads
...scribe a new algorithm, meraculous, for whole genome assembly of deep paired-end short reads, and apply it to...bp or ∼3.2 kbp, and many gaps between contigs can be closed using paired-end placements. Practical issues...2371 days ago
ONT assembly and Illumina polishing pipeline
...eline performs the following steps: Assembly of nanopore reads using Canu. Polish canu contigs using racon (optional). Map a paired-end Illumina dataset onto the con...2355 days ago
Opera: An optimal genome scaffolding program
Opera (Optimal Paired-End Read Assembler) is a sequence assembly program...ence_assembly ). It uses information from paired-end or long reads to optimally or...optimal genomic scaffolds with high-throughput paired-end sequences. Journal of Computa...2351 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 t...2349 days ago