AVID: A Global Alignment Program
A new global alignment method called AVID. The method is designed to be fast, memory efficient, and practical for sequence alignments of large genomic regions up to megabases long. W...2530 days ago
CHSMiner: a GUI tool to identify chromosomal homologous segments
...iner that detects CHSs based on shared gene content alone. It implements fast greedy search algorithm and r.... Conclusion CHSMiner is characterized by its integrated workflow, fast speed and convenient usage. I...2351 days ago
miniasm: very fast OLC-based de novo assembler for noisy long reads
Miniasm is a very fast OLC-based de novo assembler for noisy l...quality assemblies. Minimap and miniasm are ultrafast tools for (i) mapping and (ii...q reads.paf.gz > reads.gfa Convert GFA to FASTA: awk '/^S/{print ">"$2...2343 days ago
PLAST: A fast, accurate and NGS scalable bank-to-bank sequence similarity search tool
PLAST is a fast, accurate and NGS scalable bank-to-bank sequence similarity search tool providing significant accelerations of seeds-based heuristic comparison methods, suc...2339 days ago
FOGSAA: Fast Optimal Global Sequence Alignment Algorithm
...irty and the point of differences between pair of sequences. FOGSAA is a fast Global alignment algorithm. I...of sequences (protein or nucleotide) and results in an optimal alignment faster than conventional dymanic p...2331 days ago
Mugsy: multiple whole genome alignment tool
...gy from Seqan::TCoffee. Mugsy accepts draft genomes in the form of multi-FASTA files and does not require a...e genome. To cite Mugsy, use: Angiuoli SV and Salzberg SL. Mugsy: Fast multiple alignment of closely...2331 days ago
2327 days ago
Mash: fast genome and metagenome distance estimation using MinHash
Mash is normally distributed as a dependency-free binary for Linux or OSX (see https://github.com/marbl/Mash/releases). This source distribution is intended for o...2327 days ago
NanoSim: nanopore sequence read simulator based on statistical characterization.
NanoSim, a fast and scalable read simulator that captures the technology-specific features of ONT data and allows for adjustments upon improvement of nanopore sequencing te...2322 days ago
MUMmer4: A fast and versatile genome alignment system
MUMmer4, a substantially improved version of MUMmer that addresses genome size constraints by changing the 32-bit suffix tree data structure at the core of MUMmer to a...2275 days ago