mmgenome: Tools for extracting individual genomes from metagneomes
...extracting genomes in simple R functions. Thereby making the whole process of binning easy and at the same time reproducible through the Rmarkdown format. The mmgenome R package also...2104 days ago
SimLoRD: A read simulator for third generation sequencing reads
...depend on fragment length. Provided subread error probabilities are modified according to number of passes Outputs reads in FASTQ format and alignments in SAM format...2092 days ago
vcfR: a package to manipulate and visualize VCF data in R
...e intended to allow easy manipulation and visualization of variant call format (VCF) data. Functions are pro...cts matrices from the VCF data for use with typical R functions. This information can then be used for quali...2028 days ago
VGSC: A Web-Based Vector Graph Toolkit of Genome Synteny and Collinearity
VGSC, the Vector Graph toolkit of genome Synteny and Collinearity, and its online service, to visualize the synteny and collinearity in the common graphical format, including both raster (JPEG, Bitmap, and PNG) and vector graphic (SVG, EPS, and PDF).2023 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.1994 days ago
genoPlotR - plot gene and genome maps project!
...graphics of gene and genome maps. It allows the user to read from usual format such as protein table files a...eas between the segments (like Artemis, for example) Reads from common formats: Genbank, EMBL, blast, Mauve...1980 days ago
1950 days ago
UPhO: Scripts for homology and orthology assessment from genomic sequences.
...ations on its usage, installation and dependencies. Type UPhO.py -h for help. The only input requierement for UPhO is a tree (or trees) in Newick format in which the leaves are named...1947 days ago
Roary: the Pan Genome Pipeline
Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. Using a stan...1939 days ago
dotPlotly: Generate an interactive dot plot from mummer or minimap alignments
Create an interactive dot plot from mummer output OR PAF format R script that makes a plotly interactive and/or static (png/pdf) dot plot. Shiny app available for testing1909 days ago