A Post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs
...contiguate contigs from a de novo assembly against a closely related reference. IMAGE, an iterative approac...n be found here. RATT, a tool to transfer the annotation from a reference genome, or an earlier assembl...2570 days ago
SuRankCo: supervised ranking of contigs in de novo assemblies
...tion sequencing data. It trains with alignments of contigs with known reference genomes and predicts scores and ranking for contigs which have no related reference genome yet. https://bmcbioin...2558 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. Grinder can produce...2558 days ago
Genome Annotation Transfer Utility (GATU)
...program utilizes tBLASTn and BLASTn algorithms to map genes from the reference genome (the annotated strain)...a single step. ORFs present in the target genome and absent from the reference genome are also identified; t...2553 days ago
2548 days ago
GraphMap - A highly sensitive and accurate mapper for long, error-prone reads
...ing of reads for de novo assembly. Transcriptome mapping through internal construction of a transcriptome from a given genomic reference and a GTF file. &n...2544 days ago
BEDOPS v2.4.26: high-performance genomic feature operations
...genomic data. The overview section of the BEDOPS v2.4.26 documentation summarizes the toolkit, functionality and performance enhancements. The reference table offers documentation fo...2539 days ago
RNAcon: web-server for the prediction and classification of non-coding RNAs
...ediction model. The standalone version (Linux-based command-line) of RNAcon is freely available for the global scientific community. Reference: Panwar, B.; Arora, A. a...2504 days ago
QuorUM: An Error Corrector for Illumina Reads
...uccessful we are at achieving this dual goal. We evaluate the performance of QuorUM by correcting actual Illumina reads from genomes for which a reference assembly is available. QuorU...2390 days ago
DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication
...erial genome within 10 minutes, with rich information such as pseudogenes, translation exceptions, and orthologous gene assignment between given reference genomes. In addition, the mod...2384 days ago