<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/42917? https://bioinformaticsonline.com/bookmarks/view/38169/amstat-display-statistics-of-large-sequence-files-from-next-generation-sequencing-projects Fri, 09 Nov 2018 13:34:56 -0600 https://bioinformaticsonline.com/bookmarks/view/38169/amstat-display-statistics-of-large-sequence-files-from-next-generation-sequencing-projects <![CDATA[AMStat: display statistics of large sequence files from next generation sequencing projects]]> SAMStat is an efficient C program to quickly display statistics of large sequence files from next generation sequencing projects. When applied to SAM/BAM files all statistics are reported for unmapped, poorly and accurately mapped reads separately. This allows for identification of a variety of problems, such as remaining linker and adaptor sequences, causing poor mapping. Apart from this SAMStat can be used to verify individual processing steps in large analysis pipelines.

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

]]> Neel https://bioinformaticsonline.com/bookmarks/view/37674/qualimap2-evaluating-next-generation-sequencing-alignment-data Tue, 11 Sep 2018 04:44:29 -0500 https://bioinformaticsonline.com/bookmarks/view/37674/qualimap2-evaluating-next-generation-sequencing-alignment-data <![CDATA[Qualimap2: Evaluating next generation sequencing alignment data]]> Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts. 

Supported types of experiments include:

  • Whole-genome sequencing
  • Whole-exome sequencing
  • RNA-seq (speical mode available)
  • ChIP-seq

Address of the bookmark: http://qualimap.bioinfo.cipf.es/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/37830/nquire-a-statistical-framework-for-ploidy-estimation-using-next-generation-sequencing Thu, 04 Oct 2018 05:23:59 -0500 https://bioinformaticsonline.com/bookmarks/view/37830/nquire-a-statistical-framework-for-ploidy-estimation-using-next-generation-sequencing <![CDATA[nQuire: a statistical framework for ploidy estimation using next generation sequencing]]> nQuire provides a statistical framework to study organisms with intraspecific variation in ploidy. nQuire is likely to be useful in epidemiological studies of pathogens, artificial selection experiments, and for historical or ancient samples where intact nuclei are not preserved. It is implemented as a stand-alone Linux command line tool in the C programming language and is available at https://github.com/clwgg/nQuireunder the MIT license.

Address of the bookmark: https://github.com/clwgg/nQuireunder

]]> Jit https://bioinformaticsonline.com/bookmarks/view/40707/vt-a-variant-tool-set-that-discovers-short-variants-from-next-generation-sequencing-data Tue, 28 Jan 2020 03:44:43 -0600 https://bioinformaticsonline.com/bookmarks/view/40707/vt-a-variant-tool-set-that-discovers-short-variants-from-next-generation-sequencing-data <![CDATA[vt: a variant tool set that discovers short variants from Next Generation Sequencing data.]]> vt is a variant tool set that discovers short variants from Next Generation Sequencing data.

https://genome.sph.umich.edu/wiki/Vt

https://github.com/atks/vt

Address of the bookmark: https://genome.sph.umich.edu/wiki/Vt

]]> Jit https://bioinformaticsonline.com/bookmarks/view/41691/genobuntu-package-for-next-generation-sequencing-and-genome-assembly Mon, 18 May 2020 16:47:56 -0500 https://bioinformaticsonline.com/bookmarks/view/41691/genobuntu-package-for-next-generation-sequencing-and-genome-assembly <![CDATA[Genobuntu: Package for Next Generation Sequencing and Genome Assembly]]>

Genobuntu is a software package containing more than 70 software and packages oriented towards NGS. In its current version, Genobuntu supports pre assembly tools, genome assemblers as well as post assembly tools.

Commonly used biological software and example script files for different assembly pipelines have also been provided, where the example script files can be updated to suit one’s experimental needs. Genobuntu attempts to reduce the amount of time and energy needed to build software workstations and it can also act as a good teaching source for a class room setting.

Therefore, Genobuntu offers a well-tailored environment for both novices and experts working in the field of genome assembly.

Features

  • Velvet
  • MiB
  • SSAKE
  • EULER
  • VCAKE
  • ABySS
  • ALLPATHS
  • Celera
  • SHARCGS
  • Allpaths
  • IDBA
  • TAIPAN
  • Edena
  • SOAPdenovo
  • Maq
  • IDBA-UD
  • No. of Reads present in the Ref. Seq.
  • ART NGS Reads Simulator
  • HiTEC, FASTQC
  • Minimum Description Length
  • SOAPaligner
  • Sequencing Read Archive Toolkit

Address of the bookmark: https://sourceforge.net/projects/genobuntu/

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/42271/mcclintock-meta-pipeline-to-identify-transposable-element-insertions-using-next-generation-sequencing-data Tue, 27 Oct 2020 00:21:18 -0500 https://bioinformaticsonline.com/bookmarks/view/42271/mcclintock-meta-pipeline-to-identify-transposable-element-insertions-using-next-generation-sequencing-data <![CDATA[McClintock: Meta-pipeline to identify transposable element insertions using next generation sequencing data]]> an integrated bioinformatics pipeline for the detection of TE insertions in whole-genome shotgun data, called McClintock (https://github.com/bergmanlab/mcclintock), which automatically runs and standardizes output for multiple TE detection methods. We demonstrate the utility of McClintock by evaluating six TE detection methods using simulated and real genome data from the model microbial eukaryote, Saccharomyces cerevisiae. 

Address of the bookmark: https://github.com/bergmanlab/mcclintock

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/37993/platypus-a-haplotype-based-variant-caller-for-next-generation-sequence-data Thu, 25 Oct 2018 06:14:55 -0500 https://bioinformaticsonline.com/bookmarks/view/37993/platypus-a-haplotype-based-variant-caller-for-next-generation-sequence-data <![CDATA[Platypus: A Haplotype-Based Variant Caller For Next Generation Sequence Data]]> Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data. By using local realignment of reads and local assembly it achieves both high sensitivity and high specificity. Platypus can detect SNPs, MNPs, short indels, replacements and (using the assembly option) deletions up to several kb. It has been extensively tested on whole-genome, exon-capture, and targeted capture data, it has been run on very large datasets as part of the Thousand Genomes and WGS500 projects, and is being used in clinical sequencing trials in the Mainstreaming Cancer Genetics programme. 

Tutorial https://github.com/andyrimmer/Platypus/blob/master/misc/README.txt

Address of the bookmark: http://www.well.ox.ac.uk/platypus

]]> Shruti Paniwala https://bioinformaticsonline.com/bookmarks/view/37457/nanofilt-filtering-and-trimming-of-long-read-sequencing-data Mon, 30 Jul 2018 12:01:52 -0500 https://bioinformaticsonline.com/bookmarks/view/37457/nanofilt-filtering-and-trimming-of-long-read-sequencing-data <![CDATA[nanofilt: Filtering and trimming of long read sequencing data]]> Filtering on quality and/or read length, and optional trimming after passing filters.
Reads from stdin, writes to stdout.

Intended to be used:

  • directly after fastq extraction
  • prior to mapping
  • in a stream between extraction and mapping

https://github.com/wdecoster/nanofilt

Address of the bookmark: https://github.com/wdecoster/nanofilt

]]> Jit https://bioinformaticsonline.com/bookmarks/view/43892/choosing-the-right-ngs-sequencing-instrument-for-your-study Wed, 15 Jun 2022 00:37:29 -0500 https://bioinformaticsonline.com/bookmarks/view/43892/choosing-the-right-ngs-sequencing-instrument-for-your-study <![CDATA[Choosing the Right NGS Sequencing Instrument for Your Study]]> The right sequencing instrument for your study depends on your project goal. Setting aside turnaround time and price, it essentially comes down to the numbers of reads and read length you need for your experiment. Below, we've described and compared metrics for each of the instruments available. If you’re new to high-throughput sequencing and have questions about how you should design your sequencing run, fill out our free consultation form and we'll get in touch with you to help.

More at https://genohub.com/ngs-instrument-guide/

Address of the bookmark: https://genohub.com/ngs-instrument-guide/

]]> Neel https://bioinformaticsonline.com/pages/view/44672/libraries-or-management-tools-for-high-throughput-sequencing-data Fri, 04 Oct 2024 02:45:06 -0500 https://bioinformaticsonline.com/pages/view/44672/libraries-or-management-tools-for-high-throughput-sequencing-data <![CDATA[Libraries or management tools for high throughput sequencing data]]>
  • GATB Library. The Genome Analysis Toolbox with de-Bruijn graph. A large part of tools developed by the GenScale team are based on this library.
    These methods enable the analysis of data sets of any size on multi-core desktop computers, including very huge amount of reads data coming from any kind of organisms such as bacteria, plants, animals and even complex samples (e.g. metagenomes). Among them are (the full is available here: https://gatb.inria.fr/software/):
  • LRez: C++ Library and toolkit for the barcode-based management and indexation of linked-read datasets.

    • Variant calling and/or genotyping

    • DiscoSNP++ and discoSnpRAD: Reference-free small variant discovery (SNPs and indels)
    • MindTheGap: Detection and assembly of large insertion variants
    • TakeABreak: reference-free inversion discovery tool
    • SVJedi: Structural Variant genotyper with long read data
    • SVJedi-graph: Structural Variant genotyper with long read data using a variation graph

    Sequence assembly

    • MinYS: reference-guided genome assembly in metagenomics data
    • MTG-link: local assembly tool for linked-read data
    • Minia: De novo short read assembler
    • de-novo pipeline: de-novo assembly pipeline (error correction / contigs / scaffolding) for genomes and meta-genomes
    • Mapsembler2: Targeted assembly (not maintained)

    Managing k-mers & indexation

    • findere: simple strategy for speeding up queries and for reducing false positive calls from any Approximate Membership Query data structure.
      • fimpera extends findere adding the abundance information.
    • kmtricks: modular tool suite for counting kmers, and constructing Bloom filters or kmer matrices, for large collections of sequencing data.
    • kmindex is a tool for indexing and querying sequencing samples. It is built on top of kmtricks.
    • back to sequences: Find sequences (reads, unitigs, genes) related to a set of kmers in large datasets, in a matter of seconds.
    • Backpack Quotient Filter: k-mer indexing data structure with abundance
    • short read connector: Detect similar reads from potentially large read set
    • DSK: Count K-mer in sequences

    Pangenome graph manipulation

    • Pancat: Pangenome Comparison and Analysis Toolkit
    • GFAGraphs: a Python library to handle pangenome graph files in GFA format.

    Comparative metagenomics with k-mers

    Species and bacterial strains identification

    • ORI: software using long nanopore reads to identify bacteria present in a sample at the strain level
    • StrainFLAIR: STRAIN-level proFiLing using vArIation gRaph

    General-purpose sequencing data manipulation

    • GASSST: long read mapper
    • Leon: short read compressor (now included in GATB-core)
    • Bloocoo: short read corrector
    • BCALM: Construct compacted de Bruijn graphs (unitigs)

     Protein Structure

    • A_Purva: Contact Map Overlap solver
    • MD-Jeep: Distance Geometry solver
    • CSA: Comparative Structural Alignment

    Workflow

    • SLICEE: parallel execution of bioinformatics workflows

    Comparative Genomics

    • CASSIS: detection of rearrangement breakpoints
    • PLAST: intensive bank-to-bank sequence comparison
    • DRJBreakpointFinder: detection and precise localization of excision sites in proviral segments
    ]]>     LEGE