<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/41571?offset=300 https://bioinformaticsonline.com/bookmarks/view/37259/epiviz-an-interactive-visualization-tool-for-functional-genomics-data Mon, 09 Jul 2018 05:27:39 -0500 https://bioinformaticsonline.com/bookmarks/view/37259/epiviz-an-interactive-visualization-tool-for-functional-genomics-data <![CDATA[Epiviz: an interactive visualization tool for functional genomics data.]]> Epiviz is an interactive visualization tool for functional genomics data. It supports genome navigation like other genome browsers, but allows multiple visualizations of data within genomic regions using scatterplots, heatmaps and other user-supplied visualizations. It also includes data from the Gene Expression Barcode project for transcriptome visualization. It has a flexible plugin framework so users can addd3 visualizations. You can see a video tour here.

https://bioconductor.org/packages/release/bioc/html/epivizr.html

https://github.com/epiviz

https://github.com/epiviz/epiviz

Address of the bookmark: https://epiviz.github.io/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/37524/fmlrc-a-long-read-error-correction-tool-using-the-multi-string-burrows-wheeler-transform Fri, 10 Aug 2018 13:29:28 -0500 https://bioinformaticsonline.com/bookmarks/view/37524/fmlrc-a-long-read-error-correction-tool-using-the-multi-string-burrows-wheeler-transform <![CDATA[FMLRC: a long-read error correction tool using the multi-string Burrows Wheeler Transform]]> FMLRC, or FM-index Long Read Corrector, is a tool for performing hybrid correction of long read sequencing using the BWT and FM-index of short-read sequencing data. Given a BWT of the short-read sequencing data, FMLRC will build an FM-index and use that as an implicit de Bruijn graph. Each long read is then corrected independently by identifying low frequency k-mers in the long read and replacing them with the closest matching high frequency k-mers in the implicit de Bruijn graph. In contrast to other de Bruijn graph based implementations, FMLRC is not restricted to a particular k-mer size and instead uses a two pass method with both a short "k-mer" and a longer "K-mer". This allows FMLRC to correct through low complexity regions that are computational difficult for short k-mers.

Address of the bookmark: https://github.com/holtjma/fmlrc

]]> Neel 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/37837/clipcrop-a-tool-for-detecting-structural-variations-with-single-base-resolution-using-soft-clipping-information Thu, 04 Oct 2018 16:39:28 -0500 https://bioinformaticsonline.com/bookmarks/view/37837/clipcrop-a-tool-for-detecting-structural-variations-with-single-base-resolution-using-soft-clipping-information <![CDATA[ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information]]> This is a tool for detecting structural variations using soft-clipping information From SAM files.

https://github.com/shinout/clipcrop

Address of the bookmark: https://github.com/shinout/clipcrop

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/38749/clipcrop-a-tool-for-detecting-structural-variations-with-single-base-resolution-using-soft-clipping-information Sun, 20 Jan 2019 06:34:36 -0600 https://bioinformaticsonline.com/bookmarks/view/38749/clipcrop-a-tool-for-detecting-structural-variations-with-single-base-resolution-using-soft-clipping-information <![CDATA[ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information]]> ClipCrop for detecting SVs with single-base resolution using soft-clipping information. A soft-clipped sequence is an unmatched fragment in a partially mapped read. To assess the performance of ClipCrop with other SV-detecting tools, we generated various patterns of simulation data – SV lengths, read lengths, and the depth of coverage of short reads – with insertions, deletions, tandem duplications, inversions and single nucleotide alterations in a human chromosome. 

Address of the bookmark: https://github.com/shinout/clipcrop

]]> BioJoker 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/40792/haslr-a-tool-for-rapid-genome-assembly-of-long-sequencing-reads Fri, 31 Jan 2020 05:50:15 -0600 https://bioinformaticsonline.com/bookmarks/view/40792/haslr-a-tool-for-rapid-genome-assembly-of-long-sequencing-reads <![CDATA[HASLR: a tool for rapid genome assembly of long sequencing reads]]> HASLR is a tool for rapid genome assembly of long sequencing reads. HASLR is a hybrid tool which means it requires long reads generated by Third Generation Sequencing technologies (such as PacBio or Oxford Nanopore) together with Next Generation Sequencing reads (such as Illumina) from the same sample. 

Address of the bookmark: https://github.com/vpc-ccg/haslr

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