RestrictionDigest: A powerful Perl module for simulating genomic restriction digests
...yme digestion and size selection process. It can also analyze multiple genomes at one run and generates concise comparison of enzyme(s) performance across the genomes. For more information, ple...2180 days ago
MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads
...are much more efficient than the state of art of aligners and error correction tools. MECAT can be used for effectively de novo assemblying large genomes. For example, on a 32-thread...2213 days ago
Digest: In silico restriction digest of complete genomes
This tool allows to retrieve number of cleavages yielded by commercially available endonucleases in up-to-date sequenced prokaryotic genomes. When the number of fragments is bellow 50...2210 days ago
GAPPadder: A Sensitive Approach for Closing Gaps on Draft Genomes with Short Sequence Reads
...n a publication, please cite the following reference:Chong Chu, Xin Li, and Yufeng Wu. "GAPPadder: A Sensitive Approach for Closing Gaps on Draft Genomes with Short Sequence Reads." b...2210 days ago
DUPCAR: Reconstructing Contiguous Ancestral Regions with Duplications
...with duplications. The method starts from the order of genes in modern genomes and predicts predecessor and...ruct the ancestral chromosome X of placental mammals and the ancestral genomes of the ciliate Paramecium tet...2202 days ago
Hapsembler: An Assembler for Highly Polymorphic Genomes
Hapsembler is a haplotype-specific genome assembly toolkit that is designed for genomes that are rich in SNPs and other types of polymorphism. Hapsembler can be used to assemble reads from a variety of platforms including Illumina and Roche/454. http://compbio.cs.toronto.edu/hapsembler/2202 days ago
2201 days ago
GenomeMapper: Simultaneous alignment of short reads against multiple genomes
...accurate read alignments. It quickly aligns millions of reads either with ungapped or gapped alignments. It can be used to align against multiple genomes simulanteously or against a s...2198 days ago
mScaffolder: A comparative genome scaffolding tool
...genome scaffolding tool based on MUMmer mScaffolder scaffolds a genome using an existing high quality genome as the reference. It aligns the two genomes using nucmer utility from MUM...2178 days ago
CGView - Circular Genome Viewer
CGView is a Java package for generating high quality, zoomable maps of circular genomes. Its primary purpose is to serve as a component of sequence annotation pipelines, as a means of...2172 days ago