2389 days ago
2378 days ago
MUMmer4: A fast and versatile genome alignment system
...UMmer4, a substantially improved version of MUMmer that addresses genome size constraints by changing the 3...ocessing of input query sequences. With a theoretical limit on the input size of 141Tbp, MUMmer4 can now wo...2323 days ago
2311 days ago
ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data
...ed phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, an...2307 days ago
PRICE (Paired-Read Iterative Contig Extension), a de novo genome assembler implemented in C++.
...nted in C++. Its name describes the strategy that it implements for genome assembly: PRICE uses paired-read information to iteratively increase the size of existing contigs. Initiall...2195 days ago
RestrictionDigest: A powerful Perl module for simulating genomic restriction digests
...nce genome digestion and generate comprehensive information of the simulation. It can simulate single-enzyme digestion, double-enzyme digestion and size selection process. It can als...2194 days ago
FMLRC: a long-read error correction tool using the multi-string Burrows Wheeler Transform
...y k-mers in the implicit de Bruijn graph. In contrast to other de Bruijn graph based implementations, FMLRC is not restricted to a particular k-mer size and instead uses a two pass m...2135 days ago
LSC: Improving PacBio Long Read Accuracy by Short Read Alignment
...ent support. Multi-stage execution modes. Support for parallelization. Now execution proceeds in batches of long reads the size of which can be set by --long_read_batch_size N. Better compressed interme...2108 days ago
2072 days ago