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 wo...: robust and accurate haplotype assembly for diverse sequencing technologies. Genome Re...2246 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 as...2246 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/2239 days ago
bpRNA: large-scale automated annotation and analysis of RNA secondary structure
bpRNA, a novel annotation tool capable of parsing RNA structures, including complex pseudoknot-containing RNAs, to yield an objective, precise, compact, unambiguous, easily-interpretable descripti...2238 days ago
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SOAP2 : Short Oligonucleotide Analysis Package 2
...ads generated by Illumina/Solexa Genome Analyzer. Compared to soap v1...d reads onto the human reference genome. Another remarkable improveme...y a revolution in the basic data structures and algorithms used.The core...algorithms and the indexing data structures (2way-BWT) are developed by...2238 days ago
mScaffolder: A comparative genome scaffolding tool
A comparative 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...and then orders and orients the contigs of the candidate genome gu...2215 days ago
SWALO: Scaffolding with assembly likelihood optimization
SWALO (scaffolding with assembly likelihood optimization) is a method for scaffolding based on likelihood of genome assemblies computed using generative models for sequencing. Please email your questions, comments, suggestions, and bug reports to atif.bd@gmail.com.2210 days ago
minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences
git clone https://github.com/lh3/minimap2 cd minimap2 && make # long sequences against a reference genome ....2210 days ago