Results for "benchmarking and designing tools"
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CLA: Contig-Layout-Authenticator
To improve upon the shortcomings associated with the construction of dr...also hints at probable misassemblies and contaminations, for the users...draft. The CLA pipeline was designed and train...widely-used scaffolding and ordering tools using both simulated and real...2563 days ago
- This tutorial will serve as an example of how to use free and open-source genome assembly and secondary scaffolding tools to generate high quality assemblie...data, meaning that there are forward and rever...aper/blob/master/Genome%20Assembly%20and%20Annotation.md
2563 days ago
- The process of finishing a genome and moving it from a draft&n...ed the use of optical mapping and mate-pair data to augment ass...ell as source code) for these tools are freely available here:...multiple maps, contig graphs and scaffolds. Augmenting as...
2548 days ago
AVID: A Global Alignment Program
...to be fast, memory efficient, and practical for sequence alignm...arge syntenic genomic regions and whole genome human/mouse alig...with other popular alignment tools. To...representation of alignments and methods for their comparison. T...seful for future studies. The tools we have developed for the ali...2544 days ago
Grinder / Biogrinder - A versatile omics shotgun and amplicon sequencing read simulator
Grinder is a versatile program to create random shotgun and amplicon sequence libraries based on DNA, RNA...anscriptomic, proteomic, metaproteomic shotgun and ampli...be used to test the accuracy of bioinformatic tools under specific hypothesis, e....2544 days ago
Synteny Portal: a web-based application portal for synteny block analysis
Synteny Portal, a versatile web-based application portal for constructing, visualizing and browsing synteny blocks. With...owser database, (ii) visualize and download syntenic relationshi...locks with genetic information and (iv)...sating limitations of existing tools. Synteny Portal is freely ava...2544 days ago
BEDOPS v2.4.26: high-performance genomic feature operations
BEDOPS v2.4.26 is a suite of tools to address common questions raised i...— mostly with regard to overlap and proximity relationships between data sets. It aims to be scalable and flexi...summarizes the toolkit, functionality and performance enhancements. The...2525 days ago
- DESCHRAMBLER is shown to produce highly accurate reconstructions using data simulation and by benchmarking it against other reconstruction tools You can find the detail of reconstructed data at http://bioinfo.konkuk.ac.kr/DESCHRAMBLER/
2508 days ago
DIYA: a bacterial annotation pipeline for any genomics lab
DIY Genomics is an open source bioinformatics consortium intended to bring a collection of tools and libraries into the hands of small scale genomics labs for the process of sequence assembly and annotation. Projects include DIYA, MGAP, CRISPR, and DIYGV http://gmod.org/wiki/Diya2507 days ago
Mulan: MUltiple sequence Local AligNment and conservation visualization tool
Mulan performs multiple (2 or more) sequence alignments with an efficient and rapid "full local" alignment...angements (such as inversions and reshuffling) in any of the sp...refine and tba tools to align either "draft" or...sp;zPicture instructions and we refer the users to these mat...2487 days ago
