<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/38169? https://bioinformaticsonline.com/bookmarks/view/42917/fings-filters-for-next-generation-sequencing Sat, 27 Feb 2021 01:18:35 -0600 https://bioinformaticsonline.com/bookmarks/view/42917/fings-filters-for-next-generation-sequencing <![CDATA[FiNGS: Filters for Next Generation Sequencing]]> Key features
  • Filters SNVs from any variant caller to remove false positives
  • Calculates metrics based on BAM files and provides filtering not possible with other tools
  • Fully user-configurable filtering (including which filters to use and their thresholds)
  • Option to use filters identical to ICGC recommendations

FiNGS provides researchers with a tool to reproducibly filter somatic variants that is simple to both deploy and use, with filters and thresholds that are fully configurable by the user. It ingests and emits standard variant call format (VCF) files and will slot into existing sequencing pipelines. It allows users to develop and implement their own filtering strategies and simple sharing of these with others.

FiNGS reliably improves upon the precision of default variant caller outputs and performs better than other tools designed for the same task.

Address of the bookmark: https://github.com/cpwardell/FiNGS

]]> 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/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/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/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/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/37257/asar-advanced-metagenomic-sequence-analysis-in-r Mon, 09 Jul 2018 05:20:50 -0500 https://bioinformaticsonline.com/bookmarks/view/37257/asar-advanced-metagenomic-sequence-analysis-in-r <![CDATA[ASAR: Advanced metagenomic Sequence Analysis in R]]> An interactive data analysis tool for selection, aggregation and visualization of metagenomic data is presented. Functional analysis with a SEED hierarchy and pathway diagram based on KEGG orthology based upon MG-RAST annotation results is available.

To read the manual, please click the link https://askarbek-orakov.github.io/ASAR/

Address of the bookmark: https://github.com/Askarbek-orakov/ASAR

]]> Jit https://bioinformaticsonline.com/news/view/34711/1mb-long-dna-with-nanopore-technology Tue, 19 Dec 2017 18:49:28 -0600 https://bioinformaticsonline.com/news/view/34711/1mb-long-dna-with-nanopore-technology <![CDATA[1mb long DNA with Nanopore technology]]> The first continuous DNA read of more than a million bases (>1Mb) has been achieved, using Oxford Nanopore sequencing technology. Congratulations to Martin Smith and collaborators! Read more: http://bit.ly/2j5TNCO

]]> Jit https://bioinformaticsonline.com/bookmarks/view/39213/flye-fast-and-accurate-de-novo-assembler-for-single-molecule-sequencing-reads Tue, 02 Apr 2019 21:54:55 -0500 https://bioinformaticsonline.com/bookmarks/view/39213/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

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