<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/40208?offset=640 https://bioinformaticsonline.com/bookmarks/view/33976/goldgenomes-online-database Wed, 26 Jul 2017 07:49:29 -0500 https://bioinformaticsonline.com/bookmarks/view/33976/goldgenomes-online-database <![CDATA[GOLD:Genomes Online Database]]> GOLD:Genomes Online Database, is a World Wide Web resource for comprehensive access to information regarding genome and metagenome sequencing projects, and their associated metadata, around the world.

https://gold.jgi.doe.gov/

Address of the bookmark: https://gold.jgi.doe.gov/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/34482/ribbon-visualizing-complex-genome-alignments-and-structural-variation Wed, 29 Nov 2017 07:40:22 -0600 https://bioinformaticsonline.com/bookmarks/view/34482/ribbon-visualizing-complex-genome-alignments-and-structural-variation <![CDATA[Ribbon: Visualizing complex genome alignments and structural variation:]]> Ribbon can be used for long reads, short reads, paired-end reads, and assembly/genome alignments. Instructions for each data format are available by clicking on "instructions" in each tab on the right.

Local installation:

You can install Ribbon locally from Github by following the instructions here: https://github.com/MariaNattestad/Ribbon

Address of the bookmark: http://genomeribbon.com/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/34867/magic-blast-a-tool-for-mapping-large-next-generation-rna-or-dna-sequencing-runs-against-a-whole-genome-or-transcriptome Tue, 26 Dec 2017 22:23:39 -0600 https://bioinformaticsonline.com/bookmarks/view/34867/magic-blast-a-tool-for-mapping-large-next-generation-rna-or-dna-sequencing-runs-against-a-whole-genome-or-transcriptome <![CDATA[Magic-BLAST: a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome.]]> Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Each alignment optimizes a composite score, taking into account simultaneously the two reads of a pair, and in case of RNA-seq, locating the candidate introns and adding up the score of all exons. This is very different from other versions of BLAST, where each exon is scored as a separate hit and read-pairing is ignored.

Magic-BLAST incorporates within the NCBI BLAST code framework ideas developed in the NCBI Magic pipeline, in particular hit extensions by local walk and jump (http://www.ncbi.nlm.nih.gov/pubmed/26109056), and recursive clipping of mismatches near the edges of the reads, which avoids accumulating artefactual mismatches near splice sites and is needed to distinguish short indels from substitutions near the edges.

Address of the bookmark: https://ncbi.github.io/magicblast/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/36218/g-compass-a-comparative-genome-browser Thu, 12 Apr 2018 10:00:27 -0500 https://bioinformaticsonline.com/bookmarks/view/36218/g-compass-a-comparative-genome-browser <![CDATA[G-compass: a comparative genome browser]]> G-compass (http://www.h-invitational.jp/g-compass/) is a comparative genome browser. It visualizes evolutionarily conserved genomic regions between human and other 12 vertebrates based on original genome alignments pursuing higher coverage (1,2). Annotations of human genes/transcripts and their ortholog information were derived from H-InvDB and its subdatabase Evola, respectively. G-compass is available for free of charge. [ Sample ]

Address of the bookmark: http://www.h-invitational.jp/g-compass/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/36918/p-rna-scaffolder-a-fast-and-accurate-genome-scaffolder-using-paired-end-rna-sequencing-reads Tue, 12 Jun 2018 08:14:41 -0500 https://bioinformaticsonline.com/bookmarks/view/36918/p-rna-scaffolder-a-fast-and-accurate-genome-scaffolder-using-paired-end-rna-sequencing-reads <![CDATA[P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads]]> Address of the bookmark: http://www.fishbrowser.org/software/P_RNA_scaffolder/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/37416/gfinisher-a-new-strategy-to-refine-and-finish-bacterial-genome-assemblies Thu, 26 Jul 2018 09:31:55 -0500 https://bioinformaticsonline.com/bookmarks/view/37416/gfinisher-a-new-strategy-to-refine-and-finish-bacterial-genome-assemblies <![CDATA[GFinisher: a new strategy to refine and finish bacterial genome assemblies]]> GFinisher is an application tools for refinement and finalization of prokaryotic genomes assemblies using the bias of GC Skew to identify assembly errors and organizes the contigs/scaffolds with genomes references.

java -Xms2G -Xmx4G -jar GenomeFinisher.jar  \
    -i target_contigs.fasta  \
    -ds alternative_assemblies.fasta -ref reference.fasta  \
    -o outputDirectory

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

]]> Jit https://bioinformaticsonline.com/bookmarks/view/38041/synima-a-synteny-imaging-tool-for-annotated-genome-assemblies Tue, 30 Oct 2018 10:49:13 -0500 https://bioinformaticsonline.com/bookmarks/view/38041/synima-a-synteny-imaging-tool-for-annotated-genome-assemblies <![CDATA[Synima: a Synteny imaging tool for annotated genome assemblies]]> Synima written in Perl, which uses the graphical features of R. Synima takes orthologues computed from reciprocal best BLAST hits or OrthoMCL, and DAGchainer, and outputs an overview of genome-wide synteny in PDF. Each of these programs are included with the Synima package, and a pipeline for their use. Synima has a range of graphical parameters including size, colours, order, and labels, which are specified in a config file generated by the first run of Synima – and can be subsequently edited. Synima runs quickly on a command line to generate informative and publication quality figures. Synima is open source and freely available from https://github.com/rhysf/Synima under the MIT License.

Address of the bookmark: https://github.com/rhysf/Synima

]]> Abhimanyu Singh https://bioinformaticsonline.com/bookmarks/view/38224/novograph-building-whole-genome-graphs-from-long-read-based-de-novo-assemblies Thu, 15 Nov 2018 12:48:30 -0600 https://bioinformaticsonline.com/bookmarks/view/38224/novograph-building-whole-genome-graphs-from-long-read-based-de-novo-assemblies <![CDATA[NovoGraph: building whole genome graphs from long-read-based de novo assemblies]]> NovoGraph: building whole genome graphs from long-read-based de novo assemblies

An algorithmically novel approach to construct a genome graph representation of long-read-based de novo sequence assemblies. We then provide a proof of principle by creating a genome graph of seven ethnically-diverse human genomes.

 

https://f1000research.com/articles/7-1391/v1

Address of the bookmark: https://github.com/NCBI-Hackathons/NovoGraph

]]> Jit https://bioinformaticsonline.com/bookmarks/view/38672/ltr-retriever-accurately-identifies-and-annotates-ltr-retrotransposons-and-use-lai-to-evaluates-the-continuity-of-genome-assemblies Sun, 13 Jan 2019 07:14:31 -0600 https://bioinformaticsonline.com/bookmarks/view/38672/ltr-retriever-accurately-identifies-and-annotates-ltr-retrotransposons-and-use-lai-to-evaluates-the-continuity-of-genome-assemblies <![CDATA[LTR_retriever: accurately identifies and annotates LTR retrotransposons and use LAI to evaluates the continuity of genome assemblies.]]> LTR_retriever is a command line program (in Perl) for accurate identification of LTR retrotransposons (LTR-RTs) from outputs of LTRharvest, LTR_FINDER, and/or MGEScan-LTR and generating non-redundant LTR-RT library for genome annotations.

By default, the program will generate whole-genome LTR-RT annotation and the LTR Assembly Index (LAI) for evaluations of the assembly continuity of the input genome. Users can also run LAI separately (see Usage).

Address of the bookmark: https://github.com/oushujun/LTR_retriever

]]> Neel https://bioinformaticsonline.com/news/view/40416/5700-year-old-human-genome Thu, 19 Dec 2019 11:22:18 -0600 https://bioinformaticsonline.com/news/view/40416/5700-year-old-human-genome <![CDATA[5700 year-old human genome !]]> A Landmark in genomics, scientists have done something that hasn't been done ever.

Scientists have reconstructed the genome of an ancient human who lived nearly 5,700 years ago in Southern Denmark from the birch pitch- an ancient tar-like substance.

By sequencing the sample, researchers not only discovered the ancient human DNA but also microbial DNA reflecting the oral microbiome of the person who chewed the pitch, along with plant and animal DNA that could be the recent meal she might have consumed.

The DNA sample is comparable in quality to well-preserved teeth and skull bones. The DNA suggests that the chewer was a female, most likely with dark skin, dark brown hair and blue eyes.

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