2096 days ago
BASE: a practical de novo assembler for large genomes using long NGS reads
new de novo assembler called BASE. It enhances the classic seed-extension approach by indexing the reads efficiently to generate adaptive seeds that have high pr...2082 days ago
vcfR: a package to manipulate and visualize VCF data in R
VcfR is an R package intended to allow easy manipulation and visualization of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF...2076 days ago
Referee: Genome assembly quality scores
Modern genome sequencing technologies provide a succint measure of quality at each position in every read, however all of this information is lost in the assembly process....2065 days ago
BamView: a free interactive display of read alignments in BAM data files
To run the application on UNIX from the downloaded jar file run the UNIX: java -mx512m -jar BamView.jar and extra command line options are given when '-h' is used: java...2060 days ago
sim3C: Read-pair simulation of 3C-based sequencing methodologies (HiC, Meta3C, DNase-HiC)
Required python modules biopython intervaltree numpy scipy tqdm PyYAML2057 days ago
NovoGraph: building whole genome graphs from long-read-based de novo assemblies
NovoGraph: building whole genome graphs from long-read-based de novo assemblies An algorithmically novel approach to construct a genome graph representation of long-read-...2054 days ago
lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data
lordFAST is a sensitive tool for mapping long reads with high error rates. lordFAST is specially designed for aligning reads from PacBio sequencing technology but provides...2043 days ago
SISRS: Site Identification from Short Read Sequences
Next-gen sequence data such as Illumina HiSeq reads. Data must be sorted into folders by taxon (e.g. species or genus). Paired reads in fastq format must be specified by _R1 and _R2 in the (otherwise identical) filenames. Paired and unpaired reads must have a fastq file extension.2042 days ago
genoPlotR - plot gene and genome maps project!
genoPlotR is a R package to produce reproducible, publication-grade graphics of gene and genome maps. It allows the user to read from usual format such as protein table fi...2028 days ago