2412 days ago
Ribbon: Visualizing complex genome alignments and structural variation:
Ribbon can be used for long reads, short reads, paired-end reads, and assembly/geno...are available by clicking on "instructions" in each tab on the right. Local installation: You can install Ribbon locally from...2412 days ago
phyloXML: XML for evolutionary biology and comparative genomics
...gene names and identifiers, branch lengths, support values, and gene duplication and speciation events. Us...these standardized elements allows interoperability between various applications and databases. Furthermo...2412 days ago
collinearity: scripts to parse and analyse MCScanX collinearity output
scripts to parse and analyse MCScanX collinearity output2412 days ago
PLAST: A fast, accurate and NGS scalable bank-to-bank sequence similarity search tool
PLAST is a fast, accurate and NGS scalable bank-to-bank sequence sim...larity search tool providing significant accelerations of seeds-base.... PLAST stands for Parallel Local Sequence Alignment Search To...ly integrated data filtering engine capable of selecting relevant hi...2410 days ago
dnaPipeTE: de-novo assembly & annotation Pipeline for Transposable Elements
...t, Laurent Modolo and the TREEP team of the LBBE: http://lbbe.univ-lyon1.fr/-Equipe-Elements-transposables-.html?lang=en You can find the original publication in GBE here: https:/...2408 days ago
MetaSim A Sequencing Simulator for Genomics and Metagenomics.
Our software can be used to generate collections of synthetic reads that reflect the diverse taxonomical composition of typical metagenome data sets. Based...2407 days ago
Bandage: interactive visualization of de novo genome assemblies
Bandage (a Bioinformatics Application for Navigating De novo Assem...ualizing assembly graphs with connections. Users can zoom in to specific areas of...colors and extracting sequences. BLAST searches can be performed within the Band...2407 days ago
HiC-Pro: an optimized and flexible pipeline for Hi-C data processing
...o not require restriction enzyme such as DNase Hi-C. In practice, HiC-Pro can be used to process dilution Hi-C, in situ Hi-C, DNase Hi-C, Micro-C, capture-C, capture Hi-C or HiChi...2405 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) reads, to connect overlapping pair-end reads using k-mer frequencies. We evaluated our tool on 30× simulat...2405 days ago