Grinder / Biogrinder - A versatile omics shotgun and amplicon sequencing read simulator
Grinder is a versatile program to create random shotgun and amplicon sequence libraries base...scriptomic, proteomic, metaproteomic shotgun and amplicon datasets from curren...st the accuracy of bioinformatic tools under specific hypothesis, e.g. with or with...2591 days ago
2565 days ago
phyloXML: XML for evolutionary biology and comparative genomics
...e phylogenetic trees (or networks) and associated data. PhyloXML pro...taxonomic information, gene names and identifiers, branch lengths,...ility between various applications and databases. Furthermore, both...L, extensibility as well as domain specific applications are ensured. The...2401 days ago
Bandage: interactive visualization of de novo genome assemblies
Bandage (a Bioinformatics Application f...connections. Users can zoom in to specific areas of the graph and interact with it by moving no...es, adding labels, changing colors and extracting sequences. BLAST s...on of contigs alone. Availability and implementation: Source code a...2396 days ago
2390 days ago
NanoSim: nanopore sequence read simulator based on statistical characterization.
NanoSim, a fast and scalable read simulator that captures the technology-specific features of ONT data and allows for adjustments upon improv...rehensive alignment-based analysis and generates a set of read profi...nome. NanoSim is written in Python and R. The source files and manual are...2383 days ago
snakepipes: A toolkit based on snakemake and python for analysis of NGS data
snakePipes are flexible and powerful workflows built using snakemake&n...sulfite Seq/WGBS (*Also available in "allele-specific" mode) snakePipes can b...de (https://github.com/maxplanck-ie/snakepipes) and documentation (https://snakepipes....1855 days ago
Ra assembler - a de novo DNA assembler for third generation sequencing data
...ncing data developed on Faculty of Electrical Engineering and Computing (FER), Ruder Boskovic Institute (RBI) and Genome Institute of Singapore...d, it relies on detecting overlaps using a very sensitive and specific overlapper ("graphmap -w owle...2373 days ago
Rectangle Graph for Repeat Resolution in Genome Assembly
Ultimate tool for resolving repeats in genome assemblies. Though the specific implementation of the idea of the rect...2372 days ago
HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
...just work" with excellent speed and accuracy. We found that previ...bly methods are specialized for specific read technologies or pro..., HapCUT2 is designed for speed and accuracy across diverse seque...with Hi-C reads) See below for specific examples of command line options and best practices fo...2235 days ago