Cerulean: A hybrid assembly using high throughput short and long reads
Cerulean extends contigs assembled using short read datasets like Illumina paired-e...shpande, V., Fung, E. D., Pham, S., & Bafna, V. (2013). Cerulean: A hybrid assembly using high throughput short a...2299 days ago
PRICE (Paired-Read Iterative Contig Extension), a de novo genome assembler implemented in C++.
...pleased to release PRICE (Paired-Read Iterative Contig Extension), a de novo genome assembler implemented in C++. Its name describes the strategy that it implements for genome assembly: PRICE uses paired-read infor...2294 days ago
BEAP: Blast Extension and Assembly Program
The Blast Extension and Assembly Program (BEAP) is a computer program that uses a short starting DNA fragment, often a EST or partial gene segment, as "primer", to recursively blast...2294 days ago
2290 days ago
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 molecula sequencing (...ers and error correction tools. MECAT can be used for effectively de novo assemblying large genomes. For example...2325 days ago
LACHESIS: Genome Assembly with Hi-C-based Contact Probability Maps (LACHESIS)
...probability map data (e.g. from Hi-C) for chromosome-scale de novo genome assembly. Further information abo..., Kitzman JO, Shendure J#. Chromosome-scale scaffolding of de novo genome assemblies based on chroma...2322 days ago
fragScaff: Genome Assembly with Contiguity Preserving Transposition
...of contiguity information for scaffolding de novo genome assemblies. FragScaff...support robust, accurate chromosome-scale de novo genome assemblies without the...itro, long-range sequence information for de novo genome assembly via transposase contiguity.&n...2322 days ago
HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
HapCUT2 is a maximum-likelihood-based tool for assembli...racy. We found that previously described haplotype assembly methods are specialized for s...Bansal, V. HapCUT2: robust and accurate haplotype assembly for diverse sequencing techno...2320 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/2314 days ago
WhatsHap: fast and accurate read-based phasing
WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. It is especially suitable fo...2307 days ago