SMASH: An alignment-free tool to find and visualise rearrangements between pairs of DNA sequences
SMASH is a completely alignment-free method to find and visualise rearrangements between pairs of DNA sequences. The detection is based on&...2381 days ago
TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions
TRRUST contains 8,444 and 6,552 TF-target regulatory relationships of 800 human TFs and 828 mouse...for regulatory relationships from over 20 million pubmed articles, we used sentence-based tex...2381 days ago
MeDuSa: a multi-draft based scaffolder
MeDuSa (Multi-Draft based Scaffolder), an algorithm for genome scaffolding. MeDuSa exploits information obtai...orientation of the contigs. MeDuSa formalises the scaffolding pr...gorithm to solve it. In contrast to currently used scaffolde...2327 days ago
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 data. DNA-mapping* ChIP-seq* RNA-seq* ATAC-seq* s...1857 days ago
zPicture: A dynamic blastz alignment visualization
zPicture is a dynamic alignment and visualization tool that is based on blastz alignment program utilized by PipMaker. zPicture alignments can be automatically submitted to rVista 2.0 to identify conserved transcription factor binding sites.2341 days ago
CAMSA :: a tool for Comparative Analysis and Merging of Scaffold Assemblies
CAMSA – is a tool for Comparative Analysis and Merging of Scaffold Assemblies,...cense. Main features: works with any number of scaffold assem...ual assembly points) constructs a merged combined scaffold...2374 days ago
3d-dna: 3D de novo assembly (3D DNA) pipeline
This code is designed to enable anyone to reproduce the Hs2-...des aegypti genome using Hi-C yields chromosome-length scaffolds. Sci...e is described in detail in the Supporting Online Materials, specifically in the section...2374 days ago
Seal: SEquence ALignment evaluation suite
Seal is a comprehensive sequencing simulation and alignment tool evaluation suite. Th...ternatively, generating an artificial reference genome based on input...Simulating reads from random locations in the genome based on...2369 days ago
AliTV—interactive visualization of whole genome comparisons
AliTV, which provides interactive visualization of whole genome alignments. AliTV reads multiple w...ations and phylo- genetic information are supported. The user-friendly, web-browser based and...2362 days ago
mojolicious: a next generation web framework for the Perl programming language.
Back in the early days of the web, many people learned Perl because of a wonderful Perl library ca...n be used too, but may require additional CPAN modules to be installed) Fresh code based upo...2359 days ago