<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/35033? https://bioinformaticsonline.com/bookmarks/view/37645/lsc-improving-pacbio-long-read-accuracy-by-short-read-alignment Thu, 06 Sep 2018 16:27:35 -0500 https://bioinformaticsonline.com/bookmarks/view/37645/lsc-improving-pacbio-long-read-accuracy-by-short-read-alignment <![CDATA[LSC: Improving PacBio Long Read Accuracy by Short Read Alignment]]>
  • Added Command line argument support.
  • Multi-stage execution modes.
  • Support for parallelization. Now execution proceeds in batches of long reads the size of which can be set by --long_read_batch_size N.
  • Better compressed intermediate files.
  • Added utilities folder.
  • Added support for multiple short read files.
  • Removed use of configuration file.

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

    ]]>     Abhimanyu Singh     https://bioinformaticsonline.com/bookmarks/view/36950/salsa-a-tool-to-scaffold-long-read-assemblies-with-hi-c Fri, 15 Jun 2018 04:01:15 -0500 https://bioinformaticsonline.com/bookmarks/view/36950/salsa-a-tool-to-scaffold-long-read-assemblies-with-hi-c <![CDATA[SALSA: A tool to scaffold long read assemblies with Hi-C]]> Address of the bookmark: https://github.com/machinegun/SALSA

    ]]>     Jit     https://bioinformaticsonline.com/bookmarks/view/38304/lordfast-sensitive-and-fast-alignment-search-tool-for-long-noisy-read-sequencing-data Tue, 27 Nov 2018 04:43:57 -0600 https://bioinformaticsonline.com/bookmarks/view/38304/lordfast-sensitive-and-fast-alignment-search-tool-for-long-noisy-read-sequencing-data <![CDATA[lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data]]> lordFAST is a sensitive tool for mapping long reads with high error rates. lordFAST is specially designed for aligning reads from PacBio sequencing technology but provides the user the ability to change alignment parameters depending on the reads and application.

    lordFAST, a novel long-read mapper that is specifically designed to align reads generated by PacBio and potentially other SMS technologies to a reference. lordFAST not only has higher sensitivity than the available alternatives, it is also among the fastest and has a very low memory footprint.

     

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

    ]]>     BioJoker     https://bioinformaticsonline.com/bookmarks/view/37776/rhat-a-seed-and-extension-based-noisy-long-read-alignment-tool Sun, 23 Sep 2018 05:12:22 -0500 https://bioinformaticsonline.com/bookmarks/view/37776/rhat-a-seed-and-extension-based-noisy-long-read-alignment-tool <![CDATA[rHAT: a seed-and-extension-based noisy long read alignment tool]]> rHAT is a seed-and-extension-based noisy long read alignment tool. It is suitable for aligning 3rd generation sequencing reads which are in large read length with relatively high error rate, especially Pacbio's Single Molecule Read-time (SMRT) sequencing reads.

    Address of the bookmark: https://github.com/dfguan/rHAT

    ]]>     Abhimanyu Singh     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/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/31295/mycc-accurate-binning-of-metagenomic-contigs-via-automated-clustering-sequences-using-information-of-genomic-signatures-and-marker-genes Fri, 03 Mar 2017 08:34:23 -0600 https://bioinformaticsonline.com/bookmarks/view/31295/mycc-accurate-binning-of-metagenomic-contigs-via-automated-clustering-sequences-using-information-of-genomic-signatures-and-marker-genes <![CDATA[MyCC: Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes]]> MyCC, an automated binning tool that combines genomic signatures, marker genes and optional contig coverages within one or multiple samples, in order to visualize the metagenomes and to identify the reconstructed genomic fragments.

    More at http://www.nature.com/articles/srep24175

    Address of the bookmark: https://sourceforge.net/projects/sb2nhri/files/MyCC/

    ]]>     Jit     https://bioinformaticsonline.com/pages/view/33837/awesome-perl-frameworks-libraries-and-software-part-1 Fri, 07 Jul 2017 04:06:59 -0500 https://bioinformaticsonline.com/pages/view/33837/awesome-perl-frameworks-libraries-and-software-part-1 <![CDATA[Awesome perl frameworks, libraries and software - PART 1]]> A curated list of awesome Perl frameworks, libraries and software.

    ]]>     Neel     https://bioinformaticsonline.com/bookmarks/view/40969/leaflet-javascript-libraries-for-interactive-maps Mon, 10 Feb 2020 01:35:07 -0600 https://bioinformaticsonline.com/bookmarks/view/40969/leaflet-javascript-libraries-for-interactive-maps <![CDATA[Leaflet: JavaScript libraries for interactive maps]]> Leaflet is one of the most popular open-source JavaScript libraries for interactive maps.

    Features

    • Interactive panning/zooming
    • Compose maps using arbitrary combinations of:
      • Map tiles
      • Markers
      • Polygons
      • Lines
      • Popups
      • GeoJSON
    • Create maps right from the R console or RStudio
    • Embed maps in knitr/R Markdown documents and Shiny apps
    • Easily render spatial objects from the sp or sf packages, or data frames with latitude/longitude columns
    • Use map bounds and mouse events to drive Shiny logic
    • Display maps in non spherical mercator projections
    • Augment map features using chosen plugins from leaflet plugins repository

    https://rstudio.github.io/leaflet/

    Address of the bookmark: https://rstudio.github.io/leaflet/

    ]]>     Jit     https://bioinformaticsonline.com/bookmarks/view/36736/checkmassessing-the-quality-of-microbial-genomes-recovered-from-isolates-single-cells-and-metagenomes Wed, 23 May 2018 04:39:26 -0500 https://bioinformaticsonline.com/bookmarks/view/36736/checkmassessing-the-quality-of-microbial-genomes-recovered-from-isolates-single-cells-and-metagenomes <![CDATA[CheckM:Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes]]> CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. It provides robust estimates of genome completeness and contamination by using collocated sets of genes that are ubiquitous and single-copy within a phylogenetic lineage. Assessment of genome quality can also be examined using plots depicting key genomic characteristics (e.g., GC, coding density) which highlight sequences outside the expected distributions of a typical genome. CheckM also provides tools for identifying genome bins that are likely candidates for merging based on marker set compatibility, similarity in genomic characteristics, and proximity within a reference genome tree.

    Address of the bookmark: http://ecogenomics.github.io/CheckM/

    ]]>     Rahul Nayak