<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/43614?offset=100 https://bioinformaticsonline.com/bookmarks/view/37239/kat-a-k-mer-analysis-toolkit-to-quality-control-ngs-datasets-and-genome-assemblies Fri, 06 Jul 2018 03:36:45 -0500 https://bioinformaticsonline.com/bookmarks/view/37239/kat-a-k-mer-analysis-toolkit-to-quality-control-ngs-datasets-and-genome-assemblies <![CDATA[KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies]]> KAT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts. The following tools are currently available in KAT:

  • hist: Create an histogram of k-mer occurrences from a sequence file. Adds metadata in output for easy plotting.
  • gcp: K-mer GC Processor. Creates a matrix of the number of K-mers found given a GC count and a K-mer count.
  • comp: K-mer comparison tool. Creates a matrix of shared K-mers between two (or three) sequence files or hashes.
  • sect: SEquence Coverage estimator Tool. Estimates the coverage of each sequence in a file using K-mers from another sequence file.
  • blob: Given, reads and an assembly, calculates both the read and assembly K-mer coverage along with GC% for each sequence in the assembly.SEquence Coverage estimator Tool.
  • filter: Filtering tools. Contains tools for filtering k-mer hashes and FastQ/A files:
    • kmer: Produces a k-mer hash containing only k-mers within specified coverage and GC tolerances.
    • seq: Filters a sequence file based on whether or not the sequences contain k-mers within a provided hash.
  • plot: Plotting tools. Contains several plotting tools to visualise K-mer and compare distributions. The following plot tools are available:
    • density: Creates a density plot from a matrix created with the "comp" tool. Typically this is used to compare two K-mer hashes produced by different NGS reads.
    • profile: Creates a K-mer coverage plot for a single sequence. Takes in fasta coverage output coverage from the "sect" tool
    • spectra-cn: Creates a stacked histogram using a matrix created with the "comp" tool. Typically this is used to compare a jellyfish hash produced from a read set to a jellyfish hash produced from an assembly. The plot shows the amount of distinct K-mers absent, as well as the copy number variation present within the assembly.
    • spectra-hist: Creates a K-mer spectra plot for a set of K-mer histograms produced either by jellyfish-histo or kat-histo.
    • spectra-mx: Creates a K-mer spectra plot for a set of K-mer histograms that are derived from selected rows or columns in a matrix produced by the "comp".

In addition, KAT contains a python script for analysing the mathematical distributions present in the K-mer spectra in order to determine how much content is present in each peak.

This README only contains some brief details of how to install and use KAT. For more extensive documentation please visit: https://kat.readthedocs.org/en/latest/

https://academic.oup.com/bioinformatics/article/33/4/574/2664339 

Address of the bookmark: https://github.com/TGAC/KAT

]]> Jit https://bioinformaticsonline.com/bookmarks/view/27427/rcircos-an-r-package-for-circos-2d-track-plots Fri, 20 May 2016 11:01:13 -0500 https://bioinformaticsonline.com/bookmarks/view/27427/rcircos-an-r-package-for-circos-2d-track-plots <![CDATA[RCircos: an R package for Circos 2D track plots]]> RCircos package provides a simple and flexible way to make Circos 2D track plots with R and could be easily integrated into other R data processing and graphic manipulation pipelines for presenting large-scale multi-sample genomic research data. It can also serve as a base tool to generate complex Circos images.

More at https://bitbucket.org/henryhzhang/rcircos/src

Address of the bookmark: https://bitbucket.org/henryhzhang/rcircos/src

]]> Jit https://bioinformaticsonline.com/bookmarks/view/38039/vgsc-a-web-based-vector-graph-toolkit-of-genome-synteny-and-collinearity Tue, 30 Oct 2018 10:46:28 -0500 https://bioinformaticsonline.com/bookmarks/view/38039/vgsc-a-web-based-vector-graph-toolkit-of-genome-synteny-and-collinearity <![CDATA[VGSC: A Web-Based Vector Graph Toolkit of Genome Synteny and Collinearity]]> VGSC, the Vector Graph toolkit of genome Synteny and Collinearity, and its online service, to visualize the synteny and collinearity in the common graphical format, including both raster (JPEG, Bitmap, and PNG) and vector graphic (SVG, EPS, and PDF). 

Address of the bookmark: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4783527/

]]> Abhimanyu Singh https://bioinformaticsonline.com/bookmarks/view/40298/environment-for-tree-exploration-ete-is-a-python-programming-toolkit-that-assists-in-the-recontruction-manipulation-analysis-and-visualization-of-phylogenetic-trees Wed, 27 Nov 2019 05:32:33 -0600 https://bioinformaticsonline.com/bookmarks/view/40298/environment-for-tree-exploration-ete-is-a-python-programming-toolkit-that-assists-in-the-recontruction-manipulation-analysis-and-visualization-of-phylogenetic-trees <![CDATA[Environment for Tree Exploration (ETE) is a Python programming toolkit that assists in the recontruction, manipulation, analysis and visualization of phylogenetic trees]]> The Environment for Tree Exploration (ETE) is a Python programming toolkit that assists in the recontruction, manipulation, analysis and visualization of phylogenetic trees (although clustering trees or any other tree-like data structure are also supported).

Other tools

https://github.com/shenwei356/taxonkit

 

Address of the bookmark: https://pypi.org/project/ete3/3.1.1/

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/28870/genemania Mon, 22 Aug 2016 09:55:16 -0500 https://bioinformaticsonline.com/bookmarks/view/28870/genemania <![CDATA[GeneMANIA]]> Faster, more accurate algorithms function prediction "GeneMANIA (Multiple Association Network Integration Algorithm)" have however been developed in recent years and are publicly available on the web, indicating the future direction of function prediction.

Address of the bookmark: http://genemania.org/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/38515/genome-annotation-using-maker-tutorial Thu, 20 Dec 2018 17:39:23 -0600 https://bioinformaticsonline.com/bookmarks/view/38515/genome-annotation-using-maker-tutorial <![CDATA[Genome Annotation using MAKER tutorial !]]> MAKER is a great tool for annotating a reference genome using empirical and ab initiogene predictions. GMOD, the umbrella organization that includes MAKER, has some nice tutorials online for running MAKER. However, these were quite simplified examples and it took a bit of effort to wrap my head completely around everything. Here I will describe a de novo genome annotation for Boa constrictor in detail, so that there is a record and that it is easy to use this as a guide to annotate any genome.

Address of the bookmark: https://www.biostars.org/p/261203/

]]> Shruti Paniwala https://bioinformaticsonline.com/bookmarks/view/41571/wego-simple-but-useful-tool-for-visualizing-comparing-and-plotting-go-gene-ontology-annotation-results Sun, 12 Apr 2020 10:02:22 -0500 https://bioinformaticsonline.com/bookmarks/view/41571/wego-simple-but-useful-tool-for-visualizing-comparing-and-plotting-go-gene-ontology-annotation-results <![CDATA[WEGO : simple but useful tool for visualizing, comparing and plotting GO (Gene Ontology) annotation results]]> WEGO (Web Gene Ontology Annotation Plot) is a simple but useful tool for visualizing, comparing and plotting GO (Gene Ontology) annotation results. As the GO vocabulary became more and more popular, WEGO was widely adopted and used in many researches. Therefore we have updated WEGO 2.0 in 2018. Here are some changes we’ve made:
1. The limit of input file numbers was cancelled. Now the users could upload as many files as they want with one operation.
2. We have added the reference data of 9 species for users selection.
3. Besides the traditional WEGO histogram, WEGO 2.0 outputs an additional type of bar graph showing GO terms with significant gene number differences.

Address of the bookmark: http://wego.genomics.org.cn/

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/38579/genomeview-genome-browser-and-annotation-editor Wed, 02 Jan 2019 04:09:06 -0600 https://bioinformaticsonline.com/bookmarks/view/38579/genomeview-genome-browser-and-annotation-editor <![CDATA[GenomeView: genome browser and annotation editor]]> GenomeView is a genome browser and annotation editor that displays reference sequence, annotation, multiple alignments, short read alignments and graphs. Most major data formats are supported. Local and internet files can be loaded.
This project has moved to GitHub: https://github.com/GenomeView/genomeview

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

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/39869/mfannot-a-program-for-the-annotation-of-mitochondrial-and-plastid-genomes Mon, 26 Aug 2019 11:47:56 -0500 https://bioinformaticsonline.com/bookmarks/view/39869/mfannot-a-program-for-the-annotation-of-mitochondrial-and-plastid-genomes <![CDATA[MFannot : a program for the annotation of mitochondrial and plastid genomes]]> MFannot is a program for the annotation of mitochondrial and plastid genomes

MFannot is a program for the annotation of mitochondrial and plastid genomes. It is a PERL wrapper around a set of diverse, external independent tools.

It makes intense use of RNA/intron detection tools including HMMER, Exonerate, Erpin and others.

http://megasun.bch.umontreal.ca/cgi-bin/mfannot/mfannotInterface.pl

Address of the bookmark: https://github.com/BFL-lab/Mfannot

]]> Jit https://bioinformaticsonline.com/bookmarks/view/34413/coursera-genome-assembly-tutorial Sat, 25 Nov 2017 08:57:25 -0600 https://bioinformaticsonline.com/bookmarks/view/34413/coursera-genome-assembly-tutorial <![CDATA[coursera genome assembly tutorial]]> Solutions to Coursera Genome Sequencing (Bioinformatics II)

Address of the bookmark: https://github.com/iansealy/coursera-assembly

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