A Post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs
...hat is able to contiguate contigs from a de novo assembly against a closely related reference. IMAGE, an iterative approach for closing gaps in assembled genomes using mate pair infor...2564 days ago
2555 days ago
Meraculous: De Novo Genome Assembly with Short Paired-End Reads
...ived from the 15.4 megabase genome of the haploid yeast Pichia stipitis. More than 95% of the genome is recovered, with no errors; half the assembled sequence is in contigs longer...2386 days ago
miniasm: very fast OLC-based de novo assembler for noisy long reads
...sembly (on Y). They are broadly comparable. Of course, the HGAP3 consensus sequences are much more accurate. In addition, on the whole data set (assembled in ~30 min), the miniasm N50...2365 days ago
Opera: An optimal genome scaffolding program
...(http://en.wikipedia.org/wiki/Sequence_assembly ). It uses information from paired-end or long reads to optimally order and orient contigs assembled from shotgun-sequencing reads...2365 days ago
Ranbow: a haplotype assembler for polyploid genomes
...t potato genome, which is highly heterozygous. Ranbow can also be applied to other polyploid genomes. After a first phasing, Ranbow utilizes the assembled haplotypes to improve the acc...2180 days ago
“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files
...l fasta files Compute summary statistics for each TE family (number of TE copies, genome coverage...) Ambiguous cases such as nested TE can be assembled into copies automatically or...2177 days ago
Cerulean: A hybrid assembly using high throughput short and long reads
Cerulean extends contigs assembled using short read datasets like Illumina paired-end reads using long reads like PacBio RS long reads. Cerulean v0.1 has been implemented with bac...2175 days ago
HALC: High throughput algorithm for long read error correction
...hroughput than the existing algorithms while maintaining comparable accuracy. The HALC corrected long reads can thus result in 11.4-60.7% longer assembled contigs than the existing alg...2172 days ago
MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads
...e. MECAT performance were compared with PBcR-Mhap pipeline, FALCON and Canu(v1.3) in five real datasets. The quality of assembled contigs produced by MECAT is...2201 days ago