<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/44902?offset=100 https://bioinformaticsonline.com/bookmarks/view/39370/multiphate-bioinformatics-pipeline-for-functional-annotation-of-phage-isolates Thu, 16 May 2019 00:17:39 -0500 https://bioinformaticsonline.com/bookmarks/view/39370/multiphate-bioinformatics-pipeline-for-functional-annotation-of-phage-isolates <![CDATA[multiPhATE: bioinformatics pipeline for functional annotation of phage isolates]]> multiple-genome Phage Annotation Toolkit and Evaluator (multiPhATE). multiPhATE is a throughput pipeline driver that invokes an annotation pipeline (PhATE) across a user-specified set of phage genomes. This tool incorporates a de novo phage gene-calling algorithm and assigns putative functions to gene calls using protein-, virus-, and phage-centric databases. 

 

Address of the bookmark: https://github.com/carolzhou/multiPhATE

]]> Abhimanyu Singh https://bioinformaticsonline.com/bookmarks/view/42491/eukulele-taxonomic-annotation-of-the-unsung-eukaryotic-microbes Sat, 26 Dec 2020 12:10:17 -0600 https://bioinformaticsonline.com/bookmarks/view/42491/eukulele-taxonomic-annotation-of-the-unsung-eukaryotic-microbes <![CDATA[EUKulele: Taxonomic annotation of the unsung eukaryotic microbes]]>  EUKulele, an open-source software tool designed to assign taxonomy to microeukaryotes detected in meta-omic samples, and complement analysis approaches in other domains by accommodating assembly output and providing concrete metrics reporting the taxonomic completeness of each sample.

Address of the bookmark: https://github.com/AlexanderLabWHOI/EUKulele

]]> Shruti Paniwala https://bioinformaticsonline.com/bookmarks/view/36827/sex-detector-a-probabilistic-approach-to-study-sex-chromosomes-in-non-model-organisms Wed, 30 May 2018 15:57:31 -0500 https://bioinformaticsonline.com/bookmarks/view/36827/sex-detector-a-probabilistic-approach-to-study-sex-chromosomes-in-non-model-organisms <![CDATA[SEX-DETector: A Probabilistic Approach to Study Sex Chromosomes in Non-Model Organisms]]> SEX-DETector is a probabilistic method that relies on RNAseq data from a cross (parents and progeny of each sex) to infer autosomal and sex-linked genes (genes located on the non recombining part of sex chromosomes).

How does SEX-DETector work?

SEX-DETector does not require prior sequencing of a reference genome: the same sequencing data can be used for the assembly and for the mapping of the reads. A full documentation on the pipeline can be found here.

  • we recommend Trinity for the assembly.
  • Trinity components should be merged with cap3. Our code to perform the merging is available here.
  • We recommend BWA for mapping of the reads.
  • When the mapping has been perfomed, the individuals need to be genotyped; SEX-DETector takes files produced by Reads2snp (which is available for download on the PopPhyl website) as input.

Address of the bookmark: http://lbbe.univ-lyon1.fr/-SEX-DETector-.html?lang=eg

]]> Surabhi Chaudhary https://bioinformaticsonline.com/bookmarks/view/32943/npscarf-scaffolding-and-completing-assemblies-in-real-time-fashion Tue, 23 May 2017 04:53:29 -0500 https://bioinformaticsonline.com/bookmarks/view/32943/npscarf-scaffolding-and-completing-assemblies-in-real-time-fashion <![CDATA[npScarf: Scaffolding and Completing Assemblies in Real-time Fashion]]> npScarf (jsa.np.npscarf) is a program that scaffolds and completes draft genomes assemblies in real-time with Oxford Nanopore sequencing. The pipeline can run on a computing cluster as well as on a laptop computer for microbial datasets. It also facilitates the real-time analysis of positional information such as gene ordering and the detection of genes from mobile elements (plasmids and genomic islands).

Complete paper at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5321748/

Address of the bookmark: https://github.com/mdcao/npScarf

]]> Jit https://bioinformaticsonline.com/bookmarks/view/43398/waafle-a-workflow-to-annotate-assemblies-and-find-lgt-events Thu, 23 Sep 2021 14:31:06 -0500 https://bioinformaticsonline.com/bookmarks/view/43398/waafle-a-workflow-to-annotate-assemblies-and-find-lgt-events <![CDATA[WAAFLE: a Workflow to Annotate Assemblies and Find LGT Events.]]> Lateral gene transfer (LGT) is an important mechanism for genome diversification in microbial communities, including the human microbiome. While methods exist to identify LGTs from sequenced isolate genomes, identifying LGTs from community metagenomes remains an open problem. To address this, we developed WAAFLE: a Workflow to Annotate Assemblies and Find LGT Events.

Address of the bookmark: http://huttenhower.sph.harvard.edu/waafle

]]> Neel https://bioinformaticsonline.com/bookmarks/view/37414/arc-pipeline-which-facilitates-iterative-reference-guided-de-novo-assemblies Thu, 26 Jul 2018 09:20:26 -0500 https://bioinformaticsonline.com/bookmarks/view/37414/arc-pipeline-which-facilitates-iterative-reference-guided-de-novo-assemblies <![CDATA[ARC: pipeline which facilitates iterative, reference guided de novo assemblies]]> ARC is a pipeline which facilitates iterative, reference guided de novo assemblies with the intent of:

  1. Reducing time in analysis and increasing accuracy of results by only considering those reads which should assemble together.
  2. Reducing/removing reference bias as compared to mapping based approaches.

The software is designed to work in situations where a whole-genome assembly is not the objective, but rather when the researcher wishes to assemble discreet 'targets' contained within next-generation shotgun sequence data. ARC decomplexifies the traditionally difficult problem of assembly by breaking the reads into small, manageable subsets which can then be assembled quickly and efficiently in parallel. Applications include those in which the researcher wishes to de novo assemble specific content and a set of semi-similar reference targets is available to initialize the assembly process.

https://ibest.github.io/ARC/

Address of the bookmark: https://ibest.github.io/ARC/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/35907/alienness-rapid-detection-of-candidate-horizontal-gene-transfers-across-the-tree-of-life Mon, 12 Mar 2018 09:24:40 -0500 https://bioinformaticsonline.com/bookmarks/view/35907/alienness-rapid-detection-of-candidate-horizontal-gene-transfers-across-the-tree-of-life <![CDATA[alienness : Rapid Detection of Candidate Horizontal Gene Transfers across the Tree of Life]]> Horizontal gene transfer (HGT) is the transmission of genes between organisms by other means than parental to offspring inheritance. While it is prevalent in prokaryotes, HGT is less frequent in eukaryotes and particularly in Metazoa. Here, we propose Alienness, a taxonomy-aware web application available at http://alienness.sophia.inra.fr

http://www.mdpi.com/2073-4425/8/10/248

Address of the bookmark: http://alienness.sophia.inra.fr/cgi/index.cgi

]]> Jit https://bioinformaticsonline.com/bookmarks/view/34562/harvest-a-suite-of-core-genome-alignment-and-visualization-tools Fri, 08 Dec 2017 07:16:03 -0600 https://bioinformaticsonline.com/bookmarks/view/34562/harvest-a-suite-of-core-genome-alignment-and-visualization-tools <![CDATA[Harvest: a suite of core-genome alignment and visualization tools]]> Harvest is a suite of core-genome alignment and visualization tools for quickly analyzing thousands of intraspecific microbial genomes, including variant calls, recombination detection, and phylogenetic trees.

_images/screen.png

Tools

  • Parsnp - Core-genome alignment and analysis
  • Gingr - Interactive visualization of alignments, trees and variants
  • HarvestTools - Archiving and postprocessing

Address of the bookmark: https://harvest.readthedocs.io/en/latest/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/36806/manta-rapid-detection-of-structural-variants-and-indels-for-germline-and-cancer-sequencing-applications Mon, 28 May 2018 09:41:39 -0500 https://bioinformaticsonline.com/bookmarks/view/36806/manta-rapid-detection-of-structural-variants-and-indels-for-germline-and-cancer-sequencing-applications <![CDATA[Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications.]]> Address of the bookmark: https://github.com/Illumina/manta

]]> Jit https://bioinformaticsonline.com/bookmarks/view/41397/svaba-structural-variation-and-indel-detection-by-local-assembly Tue, 10 Mar 2020 07:52:15 -0500 https://bioinformaticsonline.com/bookmarks/view/41397/svaba-structural-variation-and-indel-detection-by-local-assembly <![CDATA[SvABA: Structural variation and indel detection by local assembly]]> SvABA is a method for detecting structural variants in sequencing data using genome-wide local assembly. Under the hood, SvABA uses a custom implementation of SGA (String Graph Assembler) by Jared Simpson, and BWA-MEM by Heng Li. Contigs are assembled for every 25kb window (with some small overlap) for every region in the genome. The default is to use only clipped, discordant, unmapped and indel reads, although this can be customized to any set of reads at the command line using VariantBam rules. These contigs are then immediately aligned to the reference with BWA-MEM and parsed to identify variants. Sequencing reads are then realigned to the contigs with BWA-MEM, and variants are scored by their read support.

Address of the bookmark: https://github.com/walaj/svaba

]]> Jit