<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/31382?offset=280 https://bioinformaticsonline.com/bookmarks/view/37984/baum-%E2%80%93-improving-genome-assembly-by-adaptive-unique-mapping-and-local-overlap-layout-consensus Wed, 24 Oct 2018 23:35:09 -0500 https://bioinformaticsonline.com/bookmarks/view/37984/baum-%E2%80%93-improving-genome-assembly-by-adaptive-unique-mapping-and-local-overlap-layout-consensus <![CDATA[BAUM – Improving Genome Assembly by Adaptive Unique Mapping and Local Overlap-Layout-Consensus]]> BAUM, breaks the whole genome into regions by adaptive unique mapping; then the local OLC is used to assemble each region in parallel. BAUM can: (1) perform reference-assisted assembly based on the genome of a close species; (2) or improve the results of existing assemblies that are obtained based on short or long sequencing reads. 

Address of the bookmark: http://www.zhanyuwang.xin/wordpress/index.php/2017/07/21/baum-improving-genome-assembly-by-adaptive-unique-mapping-and-local-overlap-layout-consensus/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/40208/ragoo-fast-reference-guided-scaffolding-of-genome-assembly-contigs Sun, 27 Oct 2019 00:57:23 -0500 https://bioinformaticsonline.com/bookmarks/view/40208/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. Misassembly 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

]]> Jit https://bioinformaticsonline.com/bookmarks/view/41691/genobuntu-package-for-next-generation-sequencing-and-genome-assembly Mon, 18 May 2020 16:47:56 -0500 https://bioinformaticsonline.com/bookmarks/view/41691/genobuntu-package-for-next-generation-sequencing-and-genome-assembly <![CDATA[Genobuntu: Package for Next Generation Sequencing and Genome Assembly]]>

Genobuntu is a software package containing more than 70 software and packages oriented towards NGS. In its current version, Genobuntu supports pre assembly tools, genome assemblers as well as post assembly tools.

Commonly used biological software and example script files for different assembly pipelines have also been provided, where the example script files can be updated to suit one’s experimental needs. Genobuntu attempts to reduce the amount of time and energy needed to build software workstations and it can also act as a good teaching source for a class room setting.

Therefore, Genobuntu offers a well-tailored environment for both novices and experts working in the field of genome assembly.

Features

  • Velvet
  • MiB
  • SSAKE
  • EULER
  • VCAKE
  • ABySS
  • ALLPATHS
  • Celera
  • SHARCGS
  • Allpaths
  • IDBA
  • TAIPAN
  • Edena
  • SOAPdenovo
  • Maq
  • IDBA-UD
  • No. of Reads present in the Ref. Seq.
  • ART NGS Reads Simulator
  • HiTEC, FASTQC
  • Minimum Description Length
  • SOAPaligner
  • Sequencing Read Archive Toolkit

Address of the bookmark: https://sourceforge.net/projects/genobuntu/

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/43110/quasimodo-quasispecies-metric-determination-on-omics Sat, 26 Jun 2021 15:22:56 -0500 https://bioinformaticsonline.com/bookmarks/view/43110/quasimodo-quasispecies-metric-determination-on-omics <![CDATA[QuasiModo - Quasispecies Metric Determination on Omics]]> This repository contains the scripts and pipeline that reproduces the results of the HCMV benchmarking study. In this study we evaluated genome assemblers and variant callers on 10 in vitro generated, mixed strain HCMV sequence samples, each consisting of two lab strains in different abundance ratios. This tool can also be used to evaluate assemblies and variant calling results on other similar datasets.

https://academic.oup.com/bib/article/22/3/bbaa123/5868070

Address of the bookmark: https://github.com/hzi-bifo/Quasimodo

]]> Neel https://bioinformaticsonline.com/bookmarks/view/44223/ale-assembly-likelihood-estimator Wed, 08 Mar 2023 01:39:33 -0600 https://bioinformaticsonline.com/bookmarks/view/44223/ale-assembly-likelihood-estimator <![CDATA[ALE: Assembly Likelihood Estimator]]> 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.

Address of the bookmark: https://github.com/sc932/ALE

]]> BioStar https://bioinformaticsonline.com/opportunity/view/4004/33rd-annual-convention-of-indian-association-for-cancer-research-from-13th-to-15th-february-2014 Tue, 27 Aug 2013 10:37:08 -0500 <![CDATA[33rd Annual Convention of Indian Association for Cancer Research from 13th to 15th February 2014]]> RGCB is organizing the 33rd Annual Convention of Indian Association for Cancer Research from 13th to 15th February 2014 with the theme "Discovery, Innovation and Translation in Cancer Research"

Kindly log on to conference website http://rgcb.res.in/IACR2014 for further details and timely updates and registration. We shall truly appreciate if the same be circulated among your friends, scholars and students encouraging them to participate in the meet.

http://210.212.237.38/iacrconference/

]]> https://bioinformaticsonline.com/bookmarks/view/36954/mscaffolder-a-comparative-genome-scaffolding-tool Fri, 15 Jun 2018 04:48:01 -0500 https://bioinformaticsonline.com/bookmarks/view/36954/mscaffolder-a-comparative-genome-scaffolding-tool <![CDATA[mScaffolder: A comparative genome scaffolding tool]]> A comparative genome scaffolding tool based on MUMmer

mScaffolder scaffolds a genome using an existing high quality genome as the reference. It aligns the two genomes using nucmer utility from MUMmer and then orders and orients the contigs of the candidate genome guided by their alignments to the reference genome. Please send your questions and comments to mchakrab@uci.edu.

Citation https://www.nature.com/articles/s41588-017-0010-y

Address of the bookmark: https://github.com/mahulchak/mscaffolder

]]> Jit https://bioinformaticsonline.com/bookmarks/view/40465/airlift-a-methodology-and-tool-for-comprehensively-moving-mappings-and-annotations-from-one-genome-to-another-similar-genome Mon, 23 Dec 2019 10:20:13 -0600 https://bioinformaticsonline.com/bookmarks/view/40465/airlift-a-methodology-and-tool-for-comprehensively-moving-mappings-and-annotations-from-one-genome-to-another-similar-genome <![CDATA[AirLift, a methodology and tool for comprehensively moving mappings and annotations from one genome to another similar genome]]> We propose AirLift, a methodology and tool for comprehensively moving mappings and annotations from one genome to another similar genome while maintaining the accuracy of a full mapper.

Address of the bookmark: https://github.com/CMU-SAFARI/AirLift

]]> Jit https://bioinformaticsonline.com/bookmarks/view/43867/genomeqc-a-quality-assessment-tool-for-genome-assemblies-and-gene-structure-annotations Thu, 19 May 2022 04:29:05 -0500 https://bioinformaticsonline.com/bookmarks/view/43867/genomeqc-a-quality-assessment-tool-for-genome-assemblies-and-gene-structure-annotations <![CDATA[GenomeQC: a quality assessment tool for genome assemblies and gene structure annotations]]> The GenomeQC web application is implemented in R/Shiny version 1.5.9 and Python 3.6 and is freely available at https://genomeqc.maizegdb.org/ under the GPL license. All source code and a containerized version of the GenomeQC pipeline is available in the GitHub repository https://github.com/HuffordLab/GenomeQC.

https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-6568-2

Address of the bookmark: https://github.com/HuffordLab/GenomeQC

]]> Neel https://bioinformaticsonline.com/researchlabs/view/12870/nuclear-dynamics-lab Thu, 17 Jul 2014 15:03:27 -0500 <![CDATA[Nuclear Dynamics Lab]]> Lab focus is to elucidate fundamental principles, new mechanisms, machineries and emergent properties that are involved in maintaining the genome and gene expression programmes for improvements in lifelong health and well-being for all.

More at http://www.babraham.ac.uk/our-research/nuclear-dynamics/

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