RestrictionDigest: A powerful Perl module for simulating genomic restriction digests
RestrictionDigest can simulate the reference genome digestion and generate comprehensive information...selection process. It can also analyze multiple genomes at one run and generates con...e comparison of enzyme(s) performance across the genomes...2213 days ago
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MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads
MECAT is an ultra-fast Mapping, Error Correction and de novo Assembly Tools for single...be used for effectively de novo assemblying large genomes. For example, on a 32-thread...GHz CPU , MECAT takes 9.5 days to assemble a human genome...2245 days ago
LACHESIS: Genome Assembly with Hi-C-based Contact Probability Maps (LACHESIS)
LACHESIS is method that exploits contact probability map data (e.g. from Hi-C) for chromosome-scale de novo genome assembly. Further informatio...e J#. Chromosome-scale scaffolding of de novo genome...2242 days ago
fragScaff: Genome Assembly with Contiguity Preserving Transposition
Contiguity preserving transposition and sequencing (CPT-seq) is an entirel...y information for scaffolding de novo genome assemblies. FragScaff is comp...st, accurate chromosome-scale de novo genome assemblies without the need f...ange sequence information for de novo genome...2242 days ago
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HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to "just wor...2: robust and accurate haplotype assembly for diverse sequencing technologies. Genome...2241 days ago
Circlator: automated circularization of genome assemblies using long sequencing reads
A tool to circularize genome assemblies. The algorithm and benchmarks are described in the Genome Biology manuscript. Citation: "Circlator: automated circularization of genome...2241 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/2234 days ago
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