snakepipes: A toolkit based on snakemake and python for analysis of NGS data
snakePipes are flexible and powerful workflows built using snakemake that simplify the analysis of NGS da...and documentation (https://snakepipes.readthedocs.io/en/latest/) are available online.1796 days ago
3d-dna: 3D de novo assembly (3D DNA) pipeline
This code is designed to enable anyone to reproduce the Hs2-HiC and the AaegL4 genomes reported in: Dudchenko...igure S2. The assembly procedure is described in detail in the Supporting Online M...2313 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 v...2270 days ago
Gblocks: eliminates poorly aligned positions and divergent regions of a DNA or protein alignment
Gblocks eliminates poorly aligned positions and divergent regions of a DNA or protein alignment so that it bec...elected from a protein alignment. Further information can be found in the online d...2158 days ago
GLEAN: an unsupervised learning system to integrate disparate sources of gene structure evidence
GLEAN is an unsupervised learning system to integrate disparate sources of gene structure evidence (gene model predictions, EST/protein genomic sequence alignments, SAGE/peptide tags, etc) to produce a consensus gene prediction, without prior training.2158 days ago
D-GENIES: A tool for Dotplot large Genomes in an Interactive, Efficient and Simple way
D-GENIES – for Dotplot large Genomes in an Interactive, Efficient and Simple way – is an online tool designed to compare two genomes. It supports large genome and you can interact with the dot plot...2149 days ago
RestrictionDigest: A powerful Perl module for simulating genomic restriction digests
RestrictionDigest can simulate the reference genome digestion and generate comprehensive information of the simulat...the genomes. For more information, please see the academic paper published online (...2147 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).2007 days ago
1967 days ago
Genome Annotation using MAKER tutorial !
MAKER is a great tool for annotating a reference genome using empirical and ab initiogene predictions.&nb...p;GMOD, the umbrella organization that includes MAKER, has some nice tutorials online f...1956 days ago