Meraculous: Haplotype-sensitive Assembly of Highly Heterozygous genomes.
...Generation Sequencing data geared for large genomes. It is a hybrid k-mer/read-based assembler that capitalizes on the high accuracy of Illumina sequence by eschewing an explicit erro...2361 days ago
PASA: Gene Structure Annotation and Analysis
...notation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene...re annotation consistent with the most recently available experimental sequence data. PASA also identifies an...2355 days ago
Seal: SEquence ALignment evaluation suite
Seal is a comprehensive sequencing simulation and alignment tool evaluation suite. This software (implemented in Java) provides several utilities that can be used t...2348 days ago
Alien_Hunter : prediction of putative Horizontal Gene Transfer (HGT) events
...). An IVOM approach exploits compositional biases using variable order motif distributions and captures more reliably the local composition of a sequence compared to fixed-order metho...2343 days ago
RGFA: powerful and convenient handling of assembly graphs
...of repeats and the merging of linear paths can be performed. A typical application of RGFA is the editing of a graph, to finish the assembly of a sequence, using information not availa...1601 days ago
Circoletto: visualizing sequence similarity with Circos
Circoletto, an online visualization tool based on Circos, which provides a fast, aesthetically pleasing and informative overview of sequence similarity search results. Online version...2310 days ago
2304 days ago
MMseqs2.0: ultra fast and sensitive protein search and clustering suite
MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein sequence sets. MMseqs2 is open source...Soeding J. MMseqs2 enables sensitive protein sequence searching for the analysis of...2269 days ago
Flye: Fast and accurate de novo assembler for single molecule sequencing reads
...d. After the initial assembly, Flye performs an extra repeat classification and analysis step to improve the structural accuracy of the resulting sequence. The package also includes a...2226 days ago
Metassembler: merging and optimizing de novo genome assemblies
..., if untapped, strengths and weaknesses. We present our metassembler algorithm that merges multiple assemblies of a genome into a single superior sequence.2223 days ago