CHSMiner: a GUI tool to identify chromosomal homologous segments
Background The identification of chromosomal homologous segments (CHS) within and between genomes is essential for comparative genomics. Various processes including...2411 days ago
2410 days ago
miniasm: very fast OLC-based de novo assembler for noisy long reads
...e is 105Mb; the N50 is 1.94Mb. In comparison, the HGAP3produces a 104...ad error correctors and consensus tools, miniasm may also be useful to pro...Minimap and miniasm are ultrafast tools for (i) mapping and (ii) ass...We start with an all against all comparison: minimap -Sw5 -L100...2403 days ago
PLAST: A fast, accurate and NGS scalable bank-to-bank sequence similarity search tool
...nk sequence similarity search tool providing significant accelerations of seeds-based heuristic comparison methods, such as the Blast su...cal Sequence Alignment Search Tool and is was published in B...is a general purpose sequence comparison tool providing the following benef...2399 days ago
2389 days ago
Bandage: interactive visualization of de novo genome assemblies
Bandage (a Bioinformatics Application for Navigating De novo Assembly Graphs Easily) is a tool for visualizing assembly grap...2395 days ago
COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
An efficient tool called Connecting Overlapped Pair-End (COPE) read...d reads using k-mer frequencies. We evaluated our tool on 30× simulated pair-e...ely, 10 and 2% higher than the recently published tool FLASH. When COPE is applied t...2394 days ago
ACANA: An accurate and consistent alignment tool for DNA sequences
ACANA is an accurate and consistent alignment tool for DNA sequences. ACANA is specifically designed for aligning seque...ters, particularly the gap extension score. As an accurate alignment tool, ACANA is particularly useful...2393 days ago
jobTree based python wrapper to run the genome simulation tool suite Evolver
evolverSimControl (eSC) can be used to simulate multi-chromosome genome evolution on an arbitrary phylogeny (Newick format). In addition to simply running evolver...2391 days ago
Mugsy: multiple whole genome alignment tool
Mugsy is a multiple whole genome aligner. Mugsy uses Nucmer for pairwise alignment, a custom graph based segmentation procedure for identifying collinear regions, and...2391 days ago