<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/32948?offset=270 https://bioinformaticsonline.com/bookmarks/view/37473/lsc-a-long-read-error-correction-tool Thu, 02 Aug 2018 07:39:46 -0500 https://bioinformaticsonline.com/bookmarks/view/37473/lsc-a-long-read-error-correction-tool <![CDATA[LSC :a long read error correction tool]]> Getting Started

These simple steps will help you integrate LSC into your transcriptomics analysis pipeline.

  • Read the LSC_requirements for running LSC.
  • Download and set-up the LSC package.
  • Follow the tutorial to see how LSC works on some example data.
  • Read the manual if anything is unclear.
  • You're ready, Happy LSCing!

Latest publication

Kin Fai Au, Jason Underwood, Lawrence Lee and Wing Hung Wong 
Improving PacBio Long Read Accuracy by Short Read Alignment [Manuscript] 
PLoS ONE 2012. 7(10): e46679. doi:10.1371/journal.pone.0046679

Address of the bookmark: https://www.healthcare.uiowa.edu/labs/au/LSC/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/37672/seqmonka-tool-to-visualise-and-analyse-high-throughput-mapped-sequence-data Tue, 11 Sep 2018 04:39:38 -0500 https://bioinformaticsonline.com/bookmarks/view/37672/seqmonka-tool-to-visualise-and-analyse-high-throughput-mapped-sequence-data <![CDATA[SeqMonk:A tool to visualise and analyse high throughput mapped sequence data]]> SeqMonk is a program to enable the visualisation and analysis of mapped sequence data. It was written for use with mapped next generation sequence data but can in theory be used for any dataset which can be expressed as a series of genomic positions. It's main features are:

  • Import of mapped data from mapped data (BAM/SAM/bowtie etc)
  • Creation of data groups for visualisation and analysis
  • Visualisation of mapped regions against an annotated genome.
  • Flexible quantitation of the mapped data to allow comparisons between data sets
  • Statistical analysis of data to find regions of interest
  • Creation of reports containing data and genome annotation

Address of the bookmark: http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/38449/koala-keggs-internal-annotation-tool-for-k-number-assignment-of-kegg-genes-using-ssearch-computation Wed, 12 Dec 2018 09:16:55 -0600 https://bioinformaticsonline.com/bookmarks/view/38449/koala-keggs-internal-annotation-tool-for-k-number-assignment-of-kegg-genes-using-ssearch-computation <![CDATA[KOALA: KEGG's internal annotation tool for K number assignment of KEGG GENES using SSEARCH computation]]> KOALA (KEGG Orthology And Links Annotation) is KEGG's internal annotation tool for K number assignment of KEGG GENES using SSEARCH computation. BlastKOALA and GhostKOALA assign K numbers to the user's sequence data by BLAST and GHOSTX searches, respectively, against a nonredundant set of KEGG GENES. Annotate Sequence in KEGG Mapper and Pathogen Checker in KEGG Pathogen are special interfaces to the BlastKOALA server and can be executed in an interactive mode.    See Step-by-step Instructions.

Reference: Kanehisa, M., Sato, Y., and Morishima, K. (2016) BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J. Mol. Biol. 428, 726-731. [pubmed] [pdf]

Address of the bookmark: https://www.kegg.jp/blastkoala/

]]> Abhimanyu Singh https://bioinformaticsonline.com/bookmarks/view/40359/minipolish-a-tool-for-racon-polishing-of-miniasm-assemblies Tue, 03 Dec 2019 02:40:54 -0600 https://bioinformaticsonline.com/bookmarks/view/40359/minipolish-a-tool-for-racon-polishing-of-miniasm-assemblies <![CDATA[Minipolish: A tool for Racon polishing of miniasm assemblies]]> Miniasm is a great long-read assembly tool: straight-forward, effective and very fast. However, it does not include a polishing step, so its assemblies have a high error rate – they are essentially made of stitched-together pieces of long reads.

Racon is a great polishing tool that can be used to clean up assembly errors. It's also very fast and well suited for long-read data. However, it operates on FASTA files, not the GFA graphs that miniasm makes.

That's where Minipolish comes in. With a single command, it will use Racon to polish up a miniasm assembly, while keeping the assembly in graph form.

It also takes care of some of the other nuances of polishing a miniasm assembly:

  • Adding read depth information to contigs
  • Fixing sequence truncation that can occur in Racon
  • Adding circularising links to circular contigs if not already present (so they display better in Bandage)
  • 'Rotating' circular contigs between polishing rounds to ensure clean circularisation

Address of the bookmark: https://github.com/rrwick/Minipolish

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/41920/liftoff-an-accurate-tool-that-maps-annotations-in-gff-or-gtf-between-assemblies Tue, 30 Jun 2020 21:40:52 -0500 https://bioinformaticsonline.com/bookmarks/view/41920/liftoff-an-accurate-tool-that-maps-annotations-in-gff-or-gtf-between-assemblies <![CDATA[Liftoff: an accurate tool that maps annotations in GFF or GTF between assemblies]]>  Liftoff, an accurate tool that maps annotations in GFF or GTF between assemblies of the same, or closely-related species. Unlike current coordinate lift-over tools which require a pre-generated “chain” file as input, Liftoff is a standalone tool that takes two genome assemblies and a reference annotation as input and outputs an annotation of the target genome. 

Address of the bookmark: https://github.com/agshumate/Liftoff

]]> Jit https://bioinformaticsonline.com/bookmarks/view/42362/magic-a-tool-for-predicting-transcription-factors-and-cofactors-driving-gene-sets-using-encode-data Thu, 26 Nov 2020 11:05:04 -0600 https://bioinformaticsonline.com/bookmarks/view/42362/magic-a-tool-for-predicting-transcription-factors-and-cofactors-driving-gene-sets-using-encode-data <![CDATA[MAGIC: A tool for predicting transcription factors and cofactors driving gene sets using ENCODE data]]> The algorithm presented herein, Mining Algorithm for GenetIc Controllers (MAGIC), uses ENCODE ChIP-seq data to look for statistical enrichment of TFs and cofactors in gene bodies and flanking regions in gene lists without an a priori binary classification of genes as targets or non-targets. When compared to other TF mining resources, MAGIC displayed favourable performance in predicting TFs and cofactors that drive gene changes in 4 settings:

1) A cell line expressing or lacking single TF,

2) Breast tumors divided along PAM50 designations

3) Whole brain samples from WT mice or mice lacking a single TF in a particular neuronal subtype

4) Single cell RNAseq analysis of neurons divided by Immediate Early Gene expression levels.

In summary, MAGIC is a standalone application that produces meaningful predictions of TFs and cofactors in transcriptomic experiments.

More at https://uwmadison.app.box.com/s/8j90e5h2rjrsz3bacaxnq8kor2o64vyg

Address of the bookmark: https://github.com/asroopra/MAGIC

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/44527/alvis-a-tool-for-contig-and-read-alignment-visualisation-and-chimera-detection Wed, 08 May 2024 07:02:55 -0500 https://bioinformaticsonline.com/bookmarks/view/44527/alvis-a-tool-for-contig-and-read-alignment-visualisation-and-chimera-detection <![CDATA[Alvis: a tool for contig and read ALignment VISualisation and chimera detection]]> Alvis, a simple command line tool that can generate visualisations for a number of common alignment analysis tasks. Alvis is a fast and portable tool that accepts input in a variety of alignment formats and will output production ready vector images. Additionally, Alvis will highlight potentially chimeric reads or contigs, a common source of misassemblies.

More at https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04056-0

Address of the bookmark: https://github.com/SR-Martin/alvis

]]> LEGE https://bioinformaticsonline.com/bookmarks/view/44655/ngenomesyn-an-easy-to-use-and-flexible-tool-for-publication-ready-visualization-of-syntenic-relationships-across-multiple-genomes Tue, 10 Sep 2024 04:54:55 -0500 https://bioinformaticsonline.com/bookmarks/view/44655/ngenomesyn-an-easy-to-use-and-flexible-tool-for-publication-ready-visualization-of-syntenic-relationships-across-multiple-genomes <![CDATA[NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes]]> NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes 

image

NGenomeSyn [multiple (N) Genome Synteny], for publication-ready visualization of syntenic relationships of the whole genome or local region and genomic features (e.g. repeats, structural variations, genes) across multiple genomes with a high customization. NGenomeSyn provides an easy way for its users to visualize a large amount of data with a rich layout by simply adjusting options for moving, scaling, and rotation of target genomes. Moreover, NGenomeSyn could be applied on the visualization of relationships on non-genomic data with similar input formats.

https://academic.oup.com/bioinformatics/article/39/3/btad121/7072460

Address of the bookmark: https://github.com/hewm2008/NGenomeSyn

]]> LEGE https://bioinformaticsonline.com/news/view/10810/uk-executive-accused-in-glaxosmithkline-china-probe Wed, 14 May 2014 04:55:42 -0500 https://bioinformaticsonline.com/news/view/10810/uk-executive-accused-in-glaxosmithkline-china-probe <![CDATA[UK executive accused in GlaxoSmithKline China probe]]> Mark Reilly and two other colleagues are also suspected of bribing government officials in Beijing and Shanghai, they said.

Police have handed the case over to prosecutors, officials said.

GSK said it took the allegations "very seriously" and would co-operate with the authorities over the matter.

Chinese authorities announced in July last year that they were investigating GSK, detaining four Chinese GSK executives.

http://www.bbc.com/news/world-asia-china-27403914

]]> phu https://bioinformaticsonline.com/bookmarks/view/35272/biocircosjs-is-an-open-source-interactive-javascript-library-to-interactive-display-biological-data-on-the-web Fri, 19 Jan 2018 15:03:51 -0600 https://bioinformaticsonline.com/bookmarks/view/35272/biocircosjs-is-an-open-source-interactive-javascript-library-to-interactive-display-biological-data-on-the-web <![CDATA[BioCircos.js is an open source interactive Javascript library to interactive display biological data on the web]]> BioCircos.js is an open source interactive Javascript library which provides an easy way to interactive display biological data on the web. It implements a raster-based SVG visualization using the open source Javascript framework jquery.js. BioCircos.js is multiplatform and works in all major internet browsers (Internet Explorer, Mozilla Firefox, Google Chrome, Safari, Opera). Its speed is determined by the client’s hardware and internet browser. For smoothest user experience, we recommend Google Chrome.

BioCircos.js provides SNP, CNV, HEATMAP, LINK, LINE, SCATTER, ARC, TEXT, and HISTGRAMmodules to display genome-wide genetic variations (SNPs, CNVs and chromosome rearrangement), gene expression and biomolecule interactions. BioCircos.js also provides BACKGROUND module to display background and axis circles. Tooltips showing detailed information of SVG elements are also provided.

Demo

Address of the bookmark: http://bioinfo.ibp.ac.cn/biocircos/document/index.html

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