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...2602 days ago
SuRankCo: supervised ranking of contigs in de novo assemblies
...ne learning based software to score and rank contigs from de novo assemblies of n...ext generation sequencing data. It trains with alignments of contigs with known r...genomes and predicts scores and ranking for contigs which have no related refere...2602 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 region...e comparison of assemblies to alignment of large syntenic genomi...mat for the representation of alignments and methods for their c...2602 days ago
Synteny Portal: a web-based application portal for synteny block analysis
...locks among multiple species by using prebuilt alignments in the UCSC genome brow...isualize and download syntenic relationships as high-quality images, (iii) browse...We believe that Synteny Portal will serve as a highly valuable tool that will en...2602 days ago
dbCAN: a web server and DataBase for automated Carbohydrate-active enzyme ANnotation
...genome submitted by the user; dbCAN provides an explicitly defined signature domain for each an...ll pre-computed data freely available to the public, including sequence alignments, hidden markov mod...2597 days ago
Genome Annotation Transfer Utility (GATU)
Genome Annotation Transfer Utility (GATU) was designed to facilitate quick, efficient annotation of simila...handle multiple-exon genes as well as mature peptides. Although it was designed for use with viral genomes...2597 days ago
2597 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/203857262586 days ago
GraphMap - A highly sensitive and accurate mapper for long, error-prone reads
GraphMap - A highly sensitive and accurate mapp...Mapping position agnostic to alignment parameters. Consistently very high sensitivity and precision ac...y. Various alignment strategies (semiglobal b...error correction, for which a highly sensitive overlapper is re...2588 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 dat...2583 days ago