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 contigs from...2562 days ago
CAR: Reconstructing Contiguous Regions of an Ancestral Genome
...others. Although only a few mammalian genomes are currently sequenced to high precision, our theoretical an...icate that our results are reasonably accurate and that they will become highly accurate in the foreseeable...2557 days ago
2554 days ago
Grinder / Biogrinder - A versatile omics shotgun and amplicon sequencing read simulator
...datasets can be used to test the accuracy of bioinformatic tools under specific hypothesis, e.g. with or without sequencing errors, or with low or high community diversity. Grinder...2550 days ago
Synteny Portal: a web-based application portal for synteny block analysis
...browser database, (ii) visualize and download syntenic relationships as high-quality images, (iii) browse...-use web-based interface. We believe that Synteny Portal will serve as a highly valuable tool that will ena...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/203857262535 days ago
GraphMap - A highly sensitive and accurate mapper for long, error-prone reads
GraphMap - A highly sensitive and accurate mapper for long, error-p...t parameters. Consistently very high sensitivity and precision acr...s without requiring error correction, for which a highly sensitive overlapper is req...2537 days ago
BEDOPS v2.4.26: high-performance genomic feature operations
BEDOPS v2.4.26 is a suite of tools to address common questions raised in genomic studies — mostly with regard to overlap and proximity relationships between data...2531 days ago
GeneProf: analysis of high-throughput sequencing experiment
...hat allows users to analyse data produced using high-throughput sequencing platfor...analysis for next-gen data! Some of GeneProf's highlights include: Easy-to-use...:Step-by-step workflows make it easy to analyse high-throughput data within a mini...2508 days ago
Meraculous: De Novo Genome Assembly with Short Paired-End Reads
...es. Meraculous relies on an efficient and conservative traversal of the subgraph of the k-mer (deBruijn) graph of oligonucleotides with unique high quality extensions in the dat...2384 days ago