AVID: A Global Alignment Program
A new global alignment method called AVID. The method is designed to be fast, memory efficient, and practical fo...a quantitative comparison of AVID with other popular alignment tools. To this end, we h...2550 days ago
Grinder / Biogrinder - A versatile omics shotgun and amplicon sequencing read simulator
Grinder is a versatile program to create random shotgun and amplicon sequence libraries based on DNA, RNA or pro...encing methods for a sequence-based project, e.g. should the library be paired-end or no...2550 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/203857262534 days ago
Sequence - Evolution - Function; Computational Approaches in Comparative Genomics
Sequence - Evolution - Function is an introduction to the computational approaches that play a critical role in the emerging new branch of biology known as functional gen...2476 days ago
orthodotter: Synteny plots (oxford grid)
orthodotter -h -------------------------------------------------------------------------------- orthodo...genes, default is stdin species chr-name start end species chr-name start end...2473 days ago
Meraculous: De Novo Genome Assembly with Short Paired-End Reads
We describe a new algorithm, meraculous, for whole genome assembly of deep paired-end short reads, and apply it to the assembly...r than 269 kilobases. Incorporating fosmid ends recovers entire chromosomes....between contigs can be closed using paired-end place...2383 days ago
CHSMiner: a GUI tool to identify chromosomal homologous segments
...greedy search algorithm and rigorous statistical validation, and its friendly graphical interface allows...experimentalists and bioinformaticians interested in the structure and evolution of genomes. https://...2371 days ago
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 Illum...2367 days ago
Opera: An optimal genome scaffolding program
Opera (Optimal Paired-End Read Assembler) is a sequence assembly program (http://en.w...ce_assembly ). It uses information from paired-end or long reads to optimally or...timal genomic scaffolds with high-throughput paired-end seque...2363 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 eac...2361 days ago