<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/34463?offset=180 https://bioinformaticsonline.com/bookmarks/view/41996/wgd%E2%80%94simple-command-line-tools-for-the-analysis-of-ancient-whole-genome-duplications Thu, 23 Jul 2020 05:49:45 -0500 https://bioinformaticsonline.com/bookmarks/view/41996/wgd%E2%80%94simple-command-line-tools-for-the-analysis-of-ancient-whole-genome-duplications <![CDATA[wgd—simple command line tools for the analysis of ancient whole-genome duplications]]> wgd is a easy to use command-line tool for KS distribution construction named wgd. The wgd suite provides commonly used KS and colinearity analysis workflows together with tools for modeling and visualization, rendering these analyses accessible to genomics researchers in a convenient manner.

https://academic.oup.com/bioinformatics/article/35/12/2153/5162749

Address of the bookmark: https://github.com/arzwa/wgd

]]> LEGE https://bioinformaticsonline.com/bookmarks/view/43268/kmer-a-suite-of-tools-for-dna-sequence-analysis Wed, 18 Aug 2021 00:02:54 -0500 https://bioinformaticsonline.com/bookmarks/view/43268/kmer-a-suite-of-tools-for-dna-sequence-analysis <![CDATA[Kmer: a suite of tools for DNA sequence analysis]]> More at https://help.rc.ufl.edu/doc/Kmer

This also includes:

  • A2Amapper: ATAC, Assembly to Assembly Comparision tool:
    • Comparative mapping between two genome assemblies (same species), or between two different genomes (cross species).
  • Sim4db:
    • Spliced alignment of cDNA and genomic sequences, from the same (sim4) or related (sim4cc) species. Optimized for high-throughput batched alignment.
  • LEAFF:
    • LEAFF (ahem, Let's Extract Anything From Fasta) is a utility program for working with multi-fasta files. In addition to providing random access to the base level, it includes several analysis functions.
  • Meryl:
    • An out-of-core k-mer counter. The amount of sequence that can be processed for any size k depends only on the amount of free disk space.

Address of the bookmark: https://help.rc.ufl.edu/doc/Kmer

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/43902/interactivenn-a-web-based-tool-for-the-analysis-of-sets-through-venn-diagrams Wed, 29 Jun 2022 03:22:26 -0500 https://bioinformaticsonline.com/bookmarks/view/43902/interactivenn-a-web-based-tool-for-the-analysis-of-sets-through-venn-diagrams <![CDATA[InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams]]> InteractiVenn, a more flexible tool for interacting with Venn diagrams including up to six sets. It offers a clean interface for Venn diagram construction and enables analysis of set unions while preserving the shape of the diagram. Set unions are useful to reveal differences and similarities among sets and may be guided in our tool by a tree or by a list of set unions. The tool also allows obtaining subsets’ elements, saving and loading sets for further analyses, and exporting the diagram in vector and image formats. InteractiVenn has been used to analyze two biological datasets, but it may serve set analysis in a broad range of domains.

More at https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0611-3

image

Address of the bookmark: http://www.interactivenn.net/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/44472/pipesnake-bioinformatics-best-practice-analysis-pipeline-for-phylogenomic-reconstruction Wed, 21 Feb 2024 06:19:41 -0600 https://bioinformaticsonline.com/bookmarks/view/44472/pipesnake-bioinformatics-best-practice-analysis-pipeline-for-phylogenomic-reconstruction <![CDATA[pipesnake: bioinformatics best-practice analysis pipeline for phylogenomic reconstruction]]> ausarg/pipesnake is a bioinformatics best-practice analysis pipeline for phylogenomic reconstruction starting from short-read 'second-generation' sequencing data.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies.

Address of the bookmark: https://github.com/AusARG/pipesnake

]]> LEGE https://bioinformaticsonline.com/videolist/watch/4415/a-tour-of-the-cell Tue, 10 Sep 2013 12:01:05 -0500 https://bioinformaticsonline.com/videolist/watch/4415/a-tour-of-the-cell <![CDATA[A Tour of the Cell]]> Paul Andersen takes you on a tour of the cell. He starts by explaining the difference between prokaryotic and eukaryotic cells. He also explains why cells are small but not infinitely small. He also explains how the organelles work together in a similar fashion. Intro Music Atribution Title: I4dsong_loop_main.wav Artist: CosmicD Link to sound: http://www.freesound.org/people/CosmicD/sounds/72556/ Creative Commons Atribution License]]> https://bioinformaticsonline.com/bookmarks/view/11109/expression-profiling-of-the-wheat-pathogen-zymoseptoria-tritici Tue, 27 May 2014 17:09:24 -0500 https://bioinformaticsonline.com/bookmarks/view/11109/expression-profiling-of-the-wheat-pathogen-zymoseptoria-tritici <![CDATA[Expression profiling of the wheat pathogen Zymoseptoria tritici]]> Address of the bookmark: http://gbe.oxfordjournals.org/content/early/2014/05/14/gbe.evu101.abstract

]]> Rahul Agarwal https://bioinformaticsonline.com/researchlabs/view/22403/ryan-e-mills-lab Tue, 26 May 2015 09:29:24 -0500 <![CDATA[Ryan E. Mills Lab]]> Our research group is primarily focused on the analysis of whole genome sequence data to identify genetic variation (primarily structural variation) and examine their potential functional impact in disease phenotypes. We are particularly interested in analyzing complex regions of the genome that are not easily resolved through modern sequencing approaches and which may exhibit interesting mechanistic origins.

We are also interested in the large-scale integration of genomic, expression, methylation and proteomic data sets, as well as the application of whole genome sequence analysis in clinical diagnostics.

More at http://millslab.ccmb.med.umich.edu/index.html

]]> https://bioinformaticsonline.com/bookmarks/view/41957/majiq-2-is-released Thu, 09 Jul 2020 03:06:26 -0500 https://bioinformaticsonline.com/bookmarks/view/41957/majiq-2-is-released <![CDATA[MAJIQ 2 is released !]]>  

Ability to detect, quantify, and visualize complex and de-novo splicing variations from RNASeq.

MAJIQ’s accuracy compares favorably to other algorithms.

MAJIQ 2 is *way* faster, more memory and I/O efficient

New visualization (VOILA 2.0) Ability to analyze hundreds and thousands of samples Why so negative? (Support for a confident negative set)

Finally, a major reason we are excited about MAJIQ 2.0 is that it sets the code base for many new exciting algorithmic and visualization improvements, with application to new research questions so stay tuned!

More at https://biociphers.wordpress.com/2019/04/01/majiq-2-is-out/

Address of the bookmark: https://majiq.biociphers.org/

]]> LEGE https://bioinformaticsonline.com/bookmarks/view/36476/flye-fast-and-accurate-de-novo-assembler-for-single-molecule-sequencing-reads Fri, 04 May 2018 19:16:22 -0500 https://bioinformaticsonline.com/bookmarks/view/36476/flye-fast-and-accurate-de-novo-assembler-for-single-molecule-sequencing-reads <![CDATA[Flye: Fast and accurate de novo assembler for single molecule sequencing reads]]> Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies. The algorithm uses an A-Bruijn graph to find the overlaps between reads and does not require them to be error-corrected. After the initial assembly, Flye performs an extra repeat classification and analysis step to improve the structural accuracy of the resulting sequence. The package also includes a polisher module, which produces the final assembly of high nucleotide-level quality.

Address of the bookmark: https://github.com/fenderglass/Flye

]]> Jit https://bioinformaticsonline.com/bookmarks/view/39671/flye-fast-and-accurate-de-novo-assembler-for-single-molecule-sequencing-reads Sat, 06 Jul 2019 03:48:22 -0500 https://bioinformaticsonline.com/bookmarks/view/39671/flye-fast-and-accurate-de-novo-assembler-for-single-molecule-sequencing-reads <![CDATA[Flye: Fast and accurate de novo assembler for single molecule sequencing reads]]> Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs. Flye also includes a special mode for metagenome assembly.

Address of the bookmark: https://github.com/fenderglass/Flye

]]> Rahul Nayak