<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/43374?offset=100 https://bioinformaticsonline.com/bookmarks/view/43722/crossmap-program-for-genome-coordinates-conversion-between-different-assemblies Tue, 25 Jan 2022 17:59:32 -0600 https://bioinformaticsonline.com/bookmarks/view/43722/crossmap-program-for-genome-coordinates-conversion-between-different-assemblies <![CDATA[CrossMap: program for genome coordinates conversion between different assemblies]]> CrossMap is a program for genome coordinates conversion between different assemblies (such as hg18 (NCBI36) <=> hg19 (GRCh37)). It supports commonly used file formats including BAM, CRAM, SAM, Wiggle, BigWig, BED, GFF, GTF, MAF VCF, and gVCF.

Address of the bookmark: http://crossmap.sourceforge.net/

]]> Rahul Nayak 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/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/pages/view/44352/bioinformatics-tools-for-genome-assembly Mon, 24 Jul 2023 07:04:26 -0500 https://bioinformaticsonline.com/pages/view/44352/bioinformatics-tools-for-genome-assembly <![CDATA[Bioinformatics tools for genome assembly !]]> There are numerous genome assembly tools available, each with its strengths and weaknesses. Here is a list of some widely used genome assembly tools as of my last update in September 2021:

  1. SPAdes: An assembler specifically designed for single-cell and multi-cell bacterial genomes, as well as small eukaryotic genomes.

  2. ABySS: A parallelized assembler for large genomes that uses de Bruijn graphs.

  3. Velvet: Another de Bruijn graph-based assembler optimized for short-read sequencing data.

  4. SOAPdenovo: A de Bruijn graph-based assembler designed for short reads, widely used for assembling large and complex genomes.

  5. MaSuRCA: A hybrid assembler that combines data from multiple sequencing technologies, such as Illumina and PacBio.

  6. Canu: A long-read assembler optimized for PacBio and Oxford Nanopore sequencing data.

  7. Flye: A long-read assembler suitable for bacterial and small eukaryotic genomes.

  8. SMARTdenovo: An assembler designed for long reads, particularly suited for PacBio data.

  9. SPAdes Long Read (SPAdesLR): An extension of SPAdes for long-read data, such as those from PacBio or Nanopore.

  10. Minia: An assembler optimized for low memory consumption, suitable for small and medium-sized genomes.

  11. Unicycler: A hybrid assembler that combines short and long reads for circular bacterial genome assembly.

  12. wtdbg2: A de Bruijn graph assembler for long reads, efficient for very large genomes.

  13. Shasta: A long-read assembler that uses the Overlap-Layout-Consensus approach, suitable for PacBio and Nanopore data.

  14. Sparc: An assembler designed to handle noisy long reads from Nanopore sequencing.

  15. CANA: An assembler for metagenomic data, particularly for complex and diverse microbial communities.

  16. Ra Assembler: A metagenome assembler for long reads, designed for highly complex metagenomic samples.

Please note that the field of bioinformatics is constantly evolving, and new assembly tools may have emerged since my last update. Additionally, the performance of these tools can vary depending on the characteristics of the sequencing data and the genome being assembled. When selecting an assembly tool, consider the specific requirements of your project, the available data types, and the computational resources at your disposal. Always refer to the respective tool's documentation and publications for the most up-to-date information and recommendations.

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/44549/quartet-a-telomere-to-telomere-toolkit-for-gap-free-genome-assembly-and-centromeric-repeat-identification Sat, 08 Jun 2024 15:54:36 -0500 https://bioinformaticsonline.com/bookmarks/view/44549/quartet-a-telomere-to-telomere-toolkit-for-gap-free-genome-assembly-and-centromeric-repeat-identification <![CDATA[quarTeT: a telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification.]]> quarTeT is a collection of tools for T2T genome assembly and basic analysis in automatic workflow.

Task include:

https://academic.oup.com/hr/article/10/8/uhad127/7197191?login=false 

Address of the bookmark: http://www.atcgn.com:8080/quarTeT/home.html

]]> Abhi https://bioinformaticsonline.com/view/982 Wed, 17 Jul 2013 15:25:09 -0500 https://bioinformaticsonline.com/view/982 <![CDATA[Is reference genome necessary for gene expression study in transcriptome sequencing or for variant discovery in genome sequencing?]]> Like in case of plant genomes where nature of genome is too complex and huge in size to accomplish complete de novo assembly by current sequencing technology. What would be alternate solution? Can we live in reference free world?

]]> Rahul Agarwal https://bioinformaticsonline.com/news/view/4183/320000-viruses-in-mammals-yet-to-sequenced-in-future Tue, 03 Sep 2013 08:35:30 -0500 https://bioinformaticsonline.com/news/view/4183/320000-viruses-in-mammals-yet-to-sequenced-in-future <![CDATA[320000 viruses in mammals yet to sequenced in future!!!]]> With current biological technique improvements, finally it is now possible to look at millions of unknown viruses at genomic level and understand the mechanism. According to available data, close to 70 per cent of emerging viral diseases such as HIV/AIDS, West Nile, Ebola, SARS, and influenza, are zoonoses - infections of animals that cross into humans.

To address the challenges of describing and estimating virodiversity, a team of investigators from Center for Infection and Immunity (CII) and EcoHealth Alliance began in jungles of Bangladesh - home to the flying fox.

Reference:

http://economictimes.indiatimes.com/news/news-by-industry/et-cetera/mammals-harbour-at-least-320000-new-viruses/articleshow/22253268.cms

http://www.bbc.co.uk/news/science-environment-23932400

]]> Rahul Agarwal https://bioinformaticsonline.com/videolist/watch/4960/genome-epigenome-new-understanding-of-the-pathogens-in-your-food Fri, 27 Sep 2013 11:30:45 -0500 https://bioinformaticsonline.com/videolist/watch/4960/genome-epigenome-new-understanding-of-the-pathogens-in-your-food <![CDATA[Genome + Epigenome = New Understanding of the Pathogens in Your Food]]> UC Davis's Bart Weimer describes foodborne pathogens and their proclivity for rapid genome rearrangement. The 100K Pathogen Genome Project he leads is using PacBio long-read sequencing to close genomes and analyze methylation; Weimer reports that his team has already discovered new epigenetic modifications in Salmonella and Listeria with the technology. www.pacb.com/microbe]]> https://bioinformaticsonline.com/file/view/8650/bioinformatician-duties-and-jobs Wed, 05 Mar 2014 14:32:26 -0600 https://bioinformaticsonline.com/file/view/8650/bioinformatician-duties-and-jobs <![CDATA[Bioinformatician duties and jobs !!!]]> Needle in a haystack ... ohh yes this is what bioinformatician do. We handle and analyse, Terabytes and Petabytes of genomic data on daily basis.

]]> Jitendra Narayan https://bioinformaticsonline.com/videolist/watch/11249/how-to-sequence-the-human-genome-mark-j-kiel Fri, 30 May 2014 13:24:11 -0500 https://bioinformaticsonline.com/videolist/watch/11249/how-to-sequence-the-human-genome-mark-j-kiel <![CDATA[How to sequence the human genome - Mark J. Kiel]]> View full lesson: http://ed.ted.com/lessons/how-to-sequence-the-human-genome-mark-j-kiel Your genome, every human's genome, consists of a unique DNA sequence of A's, T's, C's and G's that tell your cells how to operate. Thanks to technological advances, scientists are now able to know the sequence of letters that makes up an individual genome relatively quickly and inexpensively. Mark J. Kiel takes an in-depth look at the science behind the sequence. Lesson by Mark J. Kiel, animation by Marc Christoforidis.]]>