https://bioinformaticsonline.com/bookmarks/view/39269/ragoo-fast-reference-guided-scaffolding-of-genome-assembly-contigs Wed, 17 Apr 2019 19:45:22 -0500 https://bioinformaticsonline.com/bookmarks/view/39269/ragoo-fast-reference-guided-scaffolding-of-genome-assembly-contigs <![CDATA[RaGOO: Fast Reference-Guided Scaffolding of Genome Assembly Contigs]]> Alonge M, Soyk S, Ramakrishnan S, Wang X, Goodwin S, Sedlazeck FJ, Lippman ZB, Schatz MC: Fast and accurate reference-guided scaffolding of draft genomes. bioRxiv 2019.

RaGOO is a tool for coalescing genome assembly contigs into pseudochromosomes via minimap2 alignments to a closely related reference genome. The focus of this tool is on practicality and therefore has the following features:

  1. Good performance. On a MacBook Pro using Arabidopsis data, pseudochromosome construction takes less than a minute and the whole pipeline with SV calling takes ~2 minutes.
  2. Intact ordering and orienting of contigs.
  3. Chimeric contig correction
  4. GFF lift-over
  5. Structural variant calling with and integrated version of Assemblytics
  6. Confidence scores associated with the grouping, localization, and orientation for each contig.

Address of the bookmark: https://github.com/malonge/RaGOO

]]> BioJoker https://bioinformaticsonline.com/bookmarks/view/40573/de-novo-genome-assembly-for-illumina-data Mon, 20 Jan 2020 05:13:29 -0600 https://bioinformaticsonline.com/bookmarks/view/40573/de-novo-genome-assembly-for-illumina-data <![CDATA[De novo Genome Assembly for Illumina Data]]> 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 genomes.

https://www.melbournebioinformatics.org.au/tutorials/tutorials/assembly/assembly-protocol/

Address of the bookmark: https://www.melbournebioinformatics.org.au/tutorials/tutorials/assembly/assembly-protocol/

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/41604/synteny-and-rearrangement-identifier-syri Tue, 05 May 2020 10:37:10 -0500 https://bioinformaticsonline.com/bookmarks/view/41604/synteny-and-rearrangement-identifier-syri <![CDATA[Synteny and Rearrangement Identifier (SyRI)]]> SyRI is a comprehensive tool for predicting genomic differences between related genomes using whole-genome assemblies (WGA). The assemblies are aligned using whole-genome alignment tools, and these alignments are then used as input to SyRI. SyRI identifies syntenic path (longest set of co-linear regions), structural rearrangements (inversions, translocations, and duplications), local variations (SNPs, indels, CNVs etc) within syntenic and structural rearrangements, and un-aligned regions.

Address of the bookmark: https://schneebergerlab.github.io/syri/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/42497/genome-assembly-training-tutorial-at-galaxy Sun, 27 Dec 2020 05:25:45 -0600 https://bioinformaticsonline.com/bookmarks/view/42497/genome-assembly-training-tutorial-at-galaxy <![CDATA[Genome assembly training tutorial at Galaxy !]]> In this tutorial we assemble and annotate the genome of E. coli strain C-1. This strain is routinely used in experimental evolution studies involving bacteriophages. For instance, now classic works by Holly Wichman and Jim Bull (Bull 1997, Bull 1998, Wichman 1999) have been performed using this strain and bacteriophage phiX174.

Address of the bookmark: https://training.galaxyproject.org/training-material/topics/assembly/tutorials/unicycler-assembly/tutorial.html

]]> Jit Fatal Error.

Fatal Error.

An unrecoverable error has occurred and has been logged. Contact the site administrator with the following information:

Exception #1746712450.