<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/34493?offset=180 https://bioinformaticsonline.com/bookmarks/view/37837/clipcrop-a-tool-for-detecting-structural-variations-with-single-base-resolution-using-soft-clipping-information Thu, 04 Oct 2018 16:39:28 -0500 https://bioinformaticsonline.com/bookmarks/view/37837/clipcrop-a-tool-for-detecting-structural-variations-with-single-base-resolution-using-soft-clipping-information <![CDATA[ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information]]> This is a tool for detecting structural variations using soft-clipping information From SAM files.

https://github.com/shinout/clipcrop

Address of the bookmark: https://github.com/shinout/clipcrop

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/38749/clipcrop-a-tool-for-detecting-structural-variations-with-single-base-resolution-using-soft-clipping-information Sun, 20 Jan 2019 06:34:36 -0600 https://bioinformaticsonline.com/bookmarks/view/38749/clipcrop-a-tool-for-detecting-structural-variations-with-single-base-resolution-using-soft-clipping-information <![CDATA[ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information]]> ClipCrop for detecting SVs with single-base resolution using soft-clipping information. A soft-clipped sequence is an unmatched fragment in a partially mapped read. To assess the performance of ClipCrop with other SV-detecting tools, we generated various patterns of simulation data – SV lengths, read lengths, and the depth of coverage of short reads – with insertions, deletions, tandem duplications, inversions and single nucleotide alterations in a human chromosome. 

Address of the bookmark: https://github.com/shinout/clipcrop

]]> BioJoker https://bioinformaticsonline.com/bookmarks/view/40465/airlift-a-methodology-and-tool-for-comprehensively-moving-mappings-and-annotations-from-one-genome-to-another-similar-genome Mon, 23 Dec 2019 10:20:13 -0600 https://bioinformaticsonline.com/bookmarks/view/40465/airlift-a-methodology-and-tool-for-comprehensively-moving-mappings-and-annotations-from-one-genome-to-another-similar-genome <![CDATA[AirLift, a methodology and tool for comprehensively moving mappings and annotations from one genome to another similar genome]]> We propose AirLift, a methodology and tool for comprehensively moving mappings and annotations from one genome to another similar genome while maintaining the accuracy of a full mapper.

Address of the bookmark: https://github.com/CMU-SAFARI/AirLift

]]> Jit https://bioinformaticsonline.com/bookmarks/view/41046/iseqqc-a-tool-for-expression-based-quality-control-in-rna-sequencing Sun, 16 Feb 2020 08:47:17 -0600 https://bioinformaticsonline.com/bookmarks/view/41046/iseqqc-a-tool-for-expression-based-quality-control-in-rna-sequencing <![CDATA[iSeqQC: a tool for expression-based quality control in RNA sequencing]]> iSeqQC, an expression-based QC tool that detects outliers either produced due to variable laboratory conditions or due to dissimilarity within a phenotypic group. iSeqQC implements various statistical approaches including unsupervised clustering, agglomerative hierarchical clustering and correlation coefficients to provide insight into outliers.

http://cancerwebpa.jefferson.edu/iSeqQC/

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3399-8

Address of the bookmark: https://github.com/gkumar09/iSeqQC

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/41686/catbat-tool-for-taxonomic-classification-of-contigs-and-metagenome-assembled-genomes-mags Mon, 18 May 2020 10:53:32 -0500 https://bioinformaticsonline.com/bookmarks/view/41686/catbat-tool-for-taxonomic-classification-of-contigs-and-metagenome-assembled-genomes-mags <![CDATA[CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)]]> Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs. CAT and BAT can be run from intermediate steps if files are formated appropriately (see Usage).

Address of the bookmark: https://github.com/dutilh/CAT

]]> Jit https://bioinformaticsonline.com/bookmarks/view/42155/clustergrammer-is-a-web-based-tool-for-visualizing-high-dimensional-data-as-an-interactive-and-shareable-hierarchically-clustered-heatmap Sun, 23 Aug 2020 19:30:17 -0500 https://bioinformaticsonline.com/bookmarks/view/42155/clustergrammer-is-a-web-based-tool-for-visualizing-high-dimensional-data-as-an-interactive-and-shareable-hierarchically-clustered-heatmap <![CDATA[Clustergrammer is a web-based tool for visualizing high-dimensional data as an interactive and shareable hierarchically clustered heatmap]]> Clustergrammer is a web-based tool for visualizing high-dimensional data (e.g. a matrix) as an interactive and shareable hierarchically clustered heatmap. Clustergrammer's front end (Clustergrammer-JS) is built using D3.js and its back-end (Clustergrammer-PY) is built using Python. Clustergrammer produces highly interactive visualizations that enable intuitive exploration of high-dimensional data and has several biology-specific features (e.g. enrichment analysis, see Biology-Specific Features) to facilitate the exploration of gene-level biological data. 

Address of the bookmark: https://github.com/MaayanLab/clustergrammer

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/43263/jumbodb-tool-for-de-bruijn-graph-construction Tue, 17 Aug 2021 13:33:46 -0500 https://bioinformaticsonline.com/bookmarks/view/43263/jumbodb-tool-for-de-bruijn-graph-construction <![CDATA[JumboDB: tool for de Bruijn graph construction]]> jumboDB tool for fast de Bruijn graph construction from long sequences (reads or genomes) with very low error rate. JumboDB is not a genome assembler by itself but rather a subroutine that translates a set of reads into compressed de Bruijn graph.

More at https://github.com/AntonBankevich/jumboDB

Address of the bookmark: https://github.com/AntonBankevich/jumboDB

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/44483/baclife-an-automated-genome-mining-tool-for-identification-of-lifestyle-associated-genes Fri, 15 Mar 2024 04:59:14 -0500 https://bioinformaticsonline.com/bookmarks/view/44483/baclife-an-automated-genome-mining-tool-for-identification-of-lifestyle-associated-genes <![CDATA[bacLIFE: an automated genome mining tool for identification of lifestyle associated genes]]> bacLIFE is a streamlined computational workflow that annotates bacterial genomes and performs large-scale comparative genomics to predict bacterial lifestyles and to pinpoint candidate genes, denominated lifestyle-associated genes (LAGs), and biosynthetic gene clusters associated with each lifestyle detected. This whole process is divided into different modules:

  • Clustering module Predicts, clusters and annotates the genes of every input genome
  • Lifestyle prediction Employs a machine learning model to forecast bacterial lifestyle or other specified metadata
  • Analitical module (Shiny app) Results from the previous modules are embedded in a user-friendly interface for comprehensive and interactive comparative genomics.

You can find the complete wiki here [https://github.com/Carrion-lab/bacLIFE/wiki/bacLIFE-wiki]

Address of the bookmark: https://github.com/Carrion-lab/bacLIFE

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/44655/ngenomesyn-an-easy-to-use-and-flexible-tool-for-publication-ready-visualization-of-syntenic-relationships-across-multiple-genomes Tue, 10 Sep 2024 04:54:55 -0500 https://bioinformaticsonline.com/bookmarks/view/44655/ngenomesyn-an-easy-to-use-and-flexible-tool-for-publication-ready-visualization-of-syntenic-relationships-across-multiple-genomes <![CDATA[NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes]]> NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes 

image

NGenomeSyn [multiple (N) Genome Synteny], for publication-ready visualization of syntenic relationships of the whole genome or local region and genomic features (e.g. repeats, structural variations, genes) across multiple genomes with a high customization. NGenomeSyn provides an easy way for its users to visualize a large amount of data with a rich layout by simply adjusting options for moving, scaling, and rotation of target genomes. Moreover, NGenomeSyn could be applied on the visualization of relationships on non-genomic data with similar input formats.

https://academic.oup.com/bioinformatics/article/39/3/btad121/7072460

Address of the bookmark: https://github.com/hewm2008/NGenomeSyn

]]> LEGE https://bioinformaticsonline.com/bookmarks/view/34445/inc-seq-accurate-single-molecule-reads-using-nanopore-sequencing Mon, 27 Nov 2017 10:38:56 -0600 https://bioinformaticsonline.com/bookmarks/view/34445/inc-seq-accurate-single-molecule-reads-using-nanopore-sequencing <![CDATA[INC-Seq: accurate single molecule reads using nanopore sequencing]]> INC-Seq reads enabled accurate species-level classification, identification of species at 0.1 % abundance and robust quantification of relative abundances, providing a cheap and effective approach for pathogen detection and microbiome profiling on the MinION system.

Address of the bookmark: https://github.com/CSB5/INC-Seq

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