<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/36954? 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/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/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/36861/eagler-a-scaffolding-tool-for-long-reads Mon, 04 Jun 2018 05:26:03 -0500 https://bioinformaticsonline.com/bookmarks/view/36861/eagler-a-scaffolding-tool-for-long-reads <![CDATA[EAGLER: a scaffolding tool for long reads.]]> EAGLER is a scaffolding tool for long reads. The scaffolder takes as input a draft genome created by any NGS assembler and a set of long reads. The long reads are used to extend the contigs present in the NGS draft and possibly join overlapping contigs. EAGLER supports both PacBio and Oxford Nanopore reads.

The tool should be compatible with most UNIX flavors and has been successfully tested on the following operating systems:

  • Mac OS X 10.11.1
  • Mac OS X 10.10.3
  • Ubuntu 14.04 LTS
https://bib.irb.hr/datoteka/844447.Diplomski_2015_Luka_terbi.pdf

Address of the bookmark: https://github.com/mculinovic/EAGLER

]]> Jit https://bioinformaticsonline.com/bookmarks/view/43791/comparative-genomics-visualisation-tools Thu, 17 Feb 2022 05:37:55 -0600 https://bioinformaticsonline.com/bookmarks/view/43791/comparative-genomics-visualisation-tools <![CDATA[Comparative genomics visualisation tools !]]> Comparative genomics visualisation tools !

Address of the bookmark: https://cmdcolin.github.io/awesome-genome-visualization/?latest=true&selected=%23BRIG&tag=Comparative

]]> Neel https://bioinformaticsonline.com/bookmarks/view/37796/grsr-a-tool-for-deriving-genome-rearrangement-scenarios-from-multiple-unichromosomal-genome-sequences Fri, 28 Sep 2018 09:35:10 -0500 https://bioinformaticsonline.com/bookmarks/view/37796/grsr-a-tool-for-deriving-genome-rearrangement-scenarios-from-multiple-unichromosomal-genome-sequences <![CDATA[GRSR: a tool for deriving genome rearrangement scenarios from multiple unichromosomal genome sequences]]> GRSR is a Tool for Deriving Genome Rearrangement Scenarios for Multiple Uni-chromosomal Genomes. This tool will do the following steps:

  • Step 1. Run mugsy to get multiple sequence alignment results.
  • Step 2 & 3. Extraction of the Coordinates of Core Blocks, Construction of Synteny Blocks and Generating Signed Permutations.
  • Step 4. Generate pairwise genome rearrangement scenarios and find repeats at the breakpoints of each rearrangement events.

https://github.com/DanwangJessica/GRSR

Address of the bookmark: https://github.com/DanwangJessica/GRSR

]]> Jit https://bioinformaticsonline.com/bookmarks/view/39624/cogent-a-tool-for-reconstructing-the-coding-genome-using-high-quality-full-length-transcriptome-sequences Tue, 18 Jun 2019 05:33:04 -0500 https://bioinformaticsonline.com/bookmarks/view/39624/cogent-a-tool-for-reconstructing-the-coding-genome-using-high-quality-full-length-transcriptome-sequences <![CDATA[Cogent: a tool for reconstructing the coding genome using high-quality full-length transcriptome sequences.]]> Cogent is a tool that identifies gene families and reconstructs the coding genome using high-quality transcriptome data without a reference genome, and can be used to check assemblies for the presence of these known coding sequences.
 

Cogent is a tool for reconstructing the coding genome using high-quality full-length transcriptome sequences. It is designed to be used on Iso-Seq data and in cases where there is no reference genome or the ref genome is highly incomplete.

See a recent presentation on Cogent being applied to the Cuttlefish Iso-Seq data.

Cogent preliminary draft paper (updated 2016Dec version), Supplementary

Please see wiki for details on usage.

Address of the bookmark: https://github.com/Magdoll/Cogent

]]> Jit https://bioinformaticsonline.com/bookmarks/view/34922/camsa-a-tool-for-comparative-analysis-and-merging-of-scaffold-assemblies Thu, 28 Dec 2017 09:10:26 -0600 https://bioinformaticsonline.com/bookmarks/view/34922/camsa-a-tool-for-comparative-analysis-and-merging-of-scaffold-assemblies <![CDATA[CAMSA :: a tool for Comparative Analysis and Merging of Scaffold Assemblies]]> CAMSA – is a tool for Comparative Analysis and Merging of Scaffold Assemblies, distributed both as a standalone software package and as Python library under the MIT license.

Main features:

  1. works with any number of scaffold assemblies in de-novo non-progressive fashion
  2. allows to simultaneously work with scaffold assemblies obtained from any in silico and in vitro techniques, supporting multiple existing formats via built-in converters
  3. creates an extensive report with several comparative quality metrics (both on assembly level and on the level of individual assembly points)
  4. constructs a merged combined scaffold assembly
  5. provides an interactive framework for a visual comparative analysis of the given assemblies

Address of the bookmark: https://cblab.org/camsa/

]]> Rahul Nayak https://bioinformaticsonline.com/opportunity/view/43559/job-offer-for-a-postdoctoral-researcher-in-genomics-bioinformatics-2-years Fri, 22 Oct 2021 04:44:33 -0500 <![CDATA[Job offer for a postdoctoral researcher in genomics / bioinformatics (2 years)]]> Ongoing research in the group of Karine Van Doninck involves topics at the core of
evolutionary biology, including the evolution of sex, genome maintenance,
recombination and extreme stress resistance on different eukaryotic systems,
including rotifers, amoeba and Corbicula clams. We are employing different tools
(including experimental ecology, population genetics, phylogeny, comparative
genomics, transcriptomics, bioinformatics, molecular and cellular biology) to study
evolutionary processes at the level of populations, both experimental and natural, and
genomes.

Offer
We offer a full-time contract for two years. The contract starts between October 2021
and December 2021. The position involves no or extremely light teaching load, if the
candidate is interested. Salaries are competitive at the European level. The recruited
person will benefit from the Belgian social insurance scheme (health care, etc.) without
additional expenses.

Profile
Applicants are expected to show outstanding commitment to research and must have
obtained a PhD by the start of the position. A strong expertise in genomics is required.
More specifically, solid competences in bioinformatics (e.g. scripting pipelines) and in
genome evolution are needed. Knowledge or interest regarding recombination,
metazoan evolution, phylogenomics and population genomics is an added-value.

Application
Applications should be submitted via email to karine.van.doninck@ulb.be. The
application package should contain the following documents:
- A curriculum vitae with the complete list of publications
- A cover letter mentioning why the candidate is interested in the position
- Minimum 2 recommendation letters
Interviews: Interviews will be conducted with the selected candidates. Selected
candidates could also be invited to give a seminar to MBE ULB.
For any additional information, please contact karine.van.doninck@ulb.be

]]> https://bioinformaticsonline.com/bookmarks/view/35384/mgcv-the-microbial-genomic-context-viewer-for-comparative-genome-analysis Mon, 29 Jan 2018 04:55:46 -0600 https://bioinformaticsonline.com/bookmarks/view/35384/mgcv-the-microbial-genomic-context-viewer-for-comparative-genome-analysis <![CDATA[MGcV: the microbial genomic context viewer for comparative genome analysis]]> MGcV is an interactive web-based visalization tool tailored to facilitate small scale genome analysis. To start using MGcV:

  1. Supply your genes/genomic segments/phylogenetic tree of interest in the input-box by
  2. Click "Visualize context".

Consult the documentation to learn more about MGcV.

Address of the bookmark: http://mgcv.cmbi.ru.nl/

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