<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/42619?offset=80 https://bioinformaticsonline.com/bookmarks/view/38443/genoplotr-plot-gene-and-genome-maps-project Wed, 12 Dec 2018 08:33:41 -0600 https://bioinformaticsonline.com/bookmarks/view/38443/genoplotr-plot-gene-and-genome-maps-project <![CDATA[genoPlotR - plot gene and genome maps project!]]> genoPlotR is a R package to produce reproducible, publication-grade graphics of gene and genome maps. It allows the user to read from usual format such as protein table files and blast results, as well as home-made tabular files.

Features

  • Linear representation of several segments of DNA
  • Comparisons represented by areas between the segments (like Artemis, for example)
  • Reads from common formats: Genbank, EMBL, blast, Mauve, and from user-generated tab files
  • Plot several subsegments of the same segment on the same line, separated by a //
  • Automatic or manual placement of the segments on the plot
  • Add annotations to all the lines
  • Create smart, automatic annotations for genomes, based on gene names
  • Add a user-generated tree
  • Add a global scale or a scale to each line
  • Use user-defined graphical functions to represent genes

Address of the bookmark: http://genoplotr.r-forge.r-project.org/

]]> Abhimanyu Singh https://bioinformaticsonline.com/bookmarks/view/41814/gggenes-a-ggplot2-extension-for-drawing-gene-arrow-maps Tue, 02 Jun 2020 11:43:34 -0500 https://bioinformaticsonline.com/bookmarks/view/41814/gggenes-a-ggplot2-extension-for-drawing-gene-arrow-maps <![CDATA[gggenes: a ggplot2 extension for drawing gene arrow maps.]]> Install the stable version of gggenes from CRAN:

install.packages("gggenes")

If you want the development version, install it from GitHub:

devtools::install_github("wilkox/gggenes")

More at https://github.com/wilkox/gggenes

Address of the bookmark: http://wilkox.org/gggenes

]]> BioStar 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/opportunity/view/43046/postdoctoral-fellow-for-a-large-scale-microbial-comparative-genomics Thu, 29 Apr 2021 08:44:53 -0500 <![CDATA[postdoctoral fellow for a large-scale microbial comparative genomics !]]> Asaf Levy hiring a postdoctoral fellow for a large-scale microbial comparative genomics project at the Hebrew University of Jerusalem (Israel).
The project is a continuation of Levy Asaf et al. Nature Genetics 2018 paper.
Requirements:
1.Experience with programming in at least one programming language, preferably Python.
2.A PhD in bioinformatics/computational biology
3.At least one first authorship publication in a good journal, preferably more.
4.Good communication skills in English
5.Ability to enter and study in Israel (not applicable for Pakistani people, for example).
6.Ability to work in a team.
Please send CV to alevy@mail.huji.ac.il

]]> https://bioinformaticsonline.com/news/view/4184/zombies-like-bacteria Tue, 03 Sep 2013 08:44:15 -0500 https://bioinformaticsonline.com/news/view/4184/zombies-like-bacteria <![CDATA[Zombies like bacteria!!!]]> Do you believe in Zombies stories … Hmm confused? Don’t worry there is a news for you. Scientists from the Integrated Ocean Drilling Program have announced the findings  of the long-lived bacteria, reproducing only once every 10,000 years, which have been found in rocks 2.5km (1.5 miles) below the ocean floor that are as much as 100 million years old.

" the microbes exist in very low concentrations, of around 1,000 microbes in every tea spoon full of rock, compared with billions or trillions of bacteria that would typically be found in the same amount of soil at Earth's surface."

Reference:

http://www.bbc.co.uk/news/science-environment-23855436

 

]]> Rahul Agarwal https://bioinformaticsonline.com/bookmarks/view/28303/fancy-oneliner-for-bioinformatics Thu, 07 Jul 2016 12:05:50 -0500 https://bioinformaticsonline.com/bookmarks/view/28303/fancy-oneliner-for-bioinformatics <![CDATA[Fancy Oneliner for Bioinformatics !!]]> This webpage lists some of the one-liners that we frequently use in metagenomic analyses. You can click on the following links to browse through different topics. You can copy/paste the commands as they are in your terminal screen, provided you follow the same naming conventions and folder structures as we have. We are sharing these codes with the intention that if they are useful and help you in your analyses, then we will be appropriately credited as considerable effort has been put into devising them.

Address of the bookmark: http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/oneliners.html

]]> Poonam Mahapatra https://bioinformaticsonline.com/bookmarks/view/42132/squeezemeta-a-fully-automated-metagenomics-pipeline-from-reads-to-bins Mon, 17 Aug 2020 05:25:10 -0500 https://bioinformaticsonline.com/bookmarks/view/42132/squeezemeta-a-fully-automated-metagenomics-pipeline-from-reads-to-bins <![CDATA[SqueezeMeta: a fully automated metagenomics pipeline, from reads to bins]]> SqueezeMeta is a full automatic pipeline for metagenomics/metatranscriptomics, covering all steps of the analysis. SqueezeMeta includes multi-metagenome support allowing the co-assembly of related metagenomes and the retrieval of individual genomes via binning procedures. Thus, SqueezeMeta features several unique characteristics:

  1. Co-assembly procedure with read mapping for estimation of the abundances of genes in each metagenome
  2. Co-assembly of a large number of metagenomes via merging of individual metagenomes
  3. Includes binning and bin checking, for retrieving individual genomes
  4. The results are stored in a database, where they can be easily exported and shared, and can be inspected anywhere using a web interface.
  5. Internal checks for the assembly and binning steps inform about the consistency of contigs and bins, allowing to spot potential chimeras.
  6. Metatranscriptomic support via mapping of cDNA reads against reference metagenomes

Address of the bookmark: https://github.com/jtamames/SqueezeMeta

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/44595/squeezemeta-a-fully-automated-metagenomics-pipeline-from-reads-to-bins Sat, 06 Jul 2024 04:29:16 -0500 https://bioinformaticsonline.com/bookmarks/view/44595/squeezemeta-a-fully-automated-metagenomics-pipeline-from-reads-to-bins <![CDATA[SqueezeMeta: a fully automated metagenomics pipeline, from reads to bins]]> SqueezeMeta is a full automatic pipeline for metagenomics/metatranscriptomics, covering all steps of the analysis. SqueezeMeta includes multi-metagenome support allowing the co-assembly of related metagenomes and the retrieval of individual genomes via binning procedures. Thus, SqueezeMeta features several unique characteristics:

  1. Co-assembly procedure with read mapping for estimation of the abundances of genes in each metagenome
  2. Co-assembly of a large number of metagenomes via merging of individual metagenomes
  3. Includes binning and bin checking, for retrieving individual genomes
  4. The results are stored in a database, where they can be easily exported and shared, and can be inspected anywhere using a web interface.
  5. Internal checks for the assembly and binning steps inform about the consistency of contigs and bins, allowing to spot potential chimeras.
  6. Metatranscriptomic support via mapping of cDNA reads against reference metagenomes

Address of the bookmark: https://github.com/jtamames/SqueezeMeta

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/28805/bambus Tue, 16 Aug 2016 08:09:15 -0500 https://bioinformaticsonline.com/bookmarks/view/28805/bambus <![CDATA[Bambus]]>

Bambus 2.0, the second generation Bambus scaffolder available as an open source package. While most other scaffolders are closely tied to a specific assembly program, Bambus accepts the output from most current assemblers and provides the user with great flexibility in choosing the scaffolding parameters. In particular, Bambus is able to accept contig linking data other than specified by mate-pairs. Such sources of information include alignment to a reference genome (Bambus can directly use the output of MUMmer), physical mapping data, or information about gene synteny.

Address of the bookmark: https://www.cbcb.umd.edu/software/bambus2

]]> Jit https://bioinformaticsonline.com/opportunity/view/40771/coordinator-of-bioinformatics-core-facility-robert-koch-institute-berlin Thu, 30 Jan 2020 07:01:45 -0600 <![CDATA[Coordinator of Bioinformatics Core Facility-Robert Koch Institute Berlin]]> We are offering the following position in unit MF 1 "Bioinformatics" of department MF "Methodology and Research Infrastructure" for a

Coordinator of our Bioinformatics Core Facility (all genders)

(salary dependent on qualifications and experience in accordance with public sector wage scale [TVöD] up to grade E 14).

The contract is not limited. The position will be available immediately.
https://www.researchgate.net/job/938589_Coordinator_of_our_Bioinformatics_Core_Facility_all_genders

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