2555 days ago
A Post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs
PAGIT addresses the need for software to generate high quality draft genomes. It is based on a series of programs that we developed: ABACAS, that is able to contiguate...2548 days ago
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. CA...2545 days ago
2540 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 mega...2536 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 proteic reference sequences provided in a FASTA file. Grin...2536 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/203857262520 days ago
Omega2: metagenome assembly pipeline
Omega found overlaps between reads using a prefix/suffix hash table. The overlap graph of reads was simplified by removing transitive edges and trimming short branches....2489 days ago
orthodotter: Synteny plots (oxford grid)
orthodotter -h -------------------------------------------------------------------------------- orthodotter - Plot orthologous genes on an oxford grid. -f <...2459 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 of a dataset of paired 75-bp Illumina rea...2369 days ago