2485 days ago
Unicycler: Hybrid assembly pipeline for bacterial genomes
Unicycler is an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets where it functions as a SPAdes-optimiser. It can also assembly long-read-only...2362 days ago
miniasm: very fast OLC-based de novo assembler for noisy long reads
...fast OLC-based de novo assembler for noisy long reads. It tak...ormat. Different from mainstream assemblers, miniasm does not have a co...tep, it takes about 3 minutes to assemble a bacterial genome. Under the...addition, on the whole data set (assembled in ~30 min), the miniasm N50...2345 days ago
Meraculous: Haplotype-sensitive Assembly of Highly Heterozygous genomes.
Meraculous is a whole genome assembler for Next Generation Sequencing data geared f...arge genomes. It is a hybrid k-mer/read-based assembler that capitalizes on the high...d multi-threaded parallelization, allowing to assemble human-sized genomes on commod...2321 days ago
PASA: Gene Structure Annotation and Analysis
PASA, acronym for Program to Assemble Spliced Alignments, is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically mo...2315 days ago
Recovery of complete genomes from metagenomes
This project contains scripts and tutorials on how to assemble individual microbial genomes from metagenomes, as described in: Genome sequences of rare, uncultured bacteria obtained b...2315 days ago
Ranbow: a haplotype assembler for polyploid genomes
Ranbow is a haplotype assembler for polyploid genomes. It has been developed...es. After a first phasing, Ranbow utilizes the assembled haplotypes to improve the ac...aplotyping ranbow eval: for evaluating of the assemble haplotypes by gold standard (...2159 days ago
“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files
...ts, retrieve their sequences and get some quantitative information. Assemble RepeatMasker hits into comple...copies, genome coverage...) Ambiguous cases such as nested TE can be assembled into copies automatically or...2156 days ago
MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads
...le, on a 32-thread computer with 2.0 GHz CPU , MECAT takes 9.5 days to assemble a human genome based on 54x S...ON and Canu(v1.3) in five real datasets. The quality of assembled contigs produced by MECAT is...2180 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/2169 days ago