Shruti Paniwala
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Rectangle Graph for Repeat Resolution in Genome Assembly
By Rahul Nayak 2522 days agobioinf.spbau.ru - Ultimate tool for resolving repeats in genome assemblies. Though the specific implementation of the idea of the rectangle graph approach is already included into the current SPAdes distribution, we're also releasing the Rectangle Graph Module...The MARVEL assembler
By Jit 2394 days agogithub.com - MARVEL consists of a set of tools that facilitate the overlapping, patching, correction and assembly of noisy (not so noisy ones as well) long reads. The assembly process can be summarized as follows: overlap patch reads overlap...GMcloser: closing gaps in assemblies accurately with a likelihood-based selection of contig or...
By Shruti Paniwala 2357 days agoacademic.oup.com - GMcloser uses likelihood-based classifiers calculated from the alignment statistics between scaffolds, contigs and paired-end reads to correctly assign contigs or long reads to gap regions of scaffolds, thereby achieving accurate and efficient gap...SIMBA: a Genome Assembly Project Management System
By Neel 2186 days agoufmg-simba.sourceforge.net - SIMBA, SImple Manager for Bacterial Assemblies, is a Web interface for managing assembly projects of bacterial genomes. SIMBA was created to assist bioinformaticians to assemble bacterial genomes sequenced with NextGeneration Sequencing (NGS)...De novo Genome Assembly for Illumina Data
By Rahul Nayak 1769 days agowww.melbournebioinformatics.org.au - Written and maintained by Simon Gladman - Melbourne Bioinformatics (formerly VLSCI) Protocol Overview / Introduction In this protocol we discuss and outline the process of de novo assembly for small to medium sized...SPADes team announce new version SPADes v3.15
By BioStar 1408 days agoNew SPAdes 3.15.0.0. announced by the SPADes teamGenome Assembly Workshop 2020
By Jit 1186 days agoucdavis-bioinformatics-training.github.io - Our team offers custom bioinformatics services to academic and private organizations. We have a strong academic background with a focus on cutting edge, open source software. We replicate standard analysis pipelines (best practices) when...ALE: Assembly Likelihood Estimator
By BioStar 626 days agogithub.com - Just import the assembly, bam and ALE scores. You can convert the .ale file to a set of .wig files with ale2wiggle.py and IGV can read those directly. Depending on your genome size you may want to convert the .wig files to the BigWig format.MetaGraph: Ultra Scalable Framework for DNA Search, Alignment, Assembly
By Abhi 167 days agometagraph.ethz.ch - The MetaGraph framework is designed to work with a wide range of input data sets, indexing from a few samples up to the contents of entire archives with hundreds of thousands of records. The indexing workflow always follows the same principle,...Demo 4: Using BLAST/BLAT in Ensembl
By Radha Agarkar 4092 days agoWe demonstrate the BLAST/BLAT tool in Ensembl. Search for a sequence in Ensembl, and identify hits to the genome, or to genes, with this tool.
