BOL: Related items

NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes

LEGE — Tue, 10 Sep 2024 04:54:55 -0500

NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes

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

How Genes are Regulated: Transcription Factors

Thu, 05 Sep 2013 16:54:19 -0500

Each cell in our body inherits the same master copy of DNA, but different cell types use it differently. Transcription Factors help influence which genes are used in which cell. Understanding how these dynamic proteins physically interact with DNA allows us to better understand and model their binding to DNA and their regulation of gene expression. Scientific Direction by the Wasserman Lab at the University of British Columbia: http://www.cmmt.ubc.ca/research/investigators/wasserman/lab Animation and editing by Blair Lyons of Stroma Studios: http://www.stromastudios.com

Ensembl 94 is out!

Jit — Fri, 26 Oct 2018 08:14:24 -0500

The latest version of Ensembl, release 94, is out and have we got some treats for you. As well as GENCODE updates for human and mouse, we’ve also got loads of new fish. Plus, we have brand new transcription factor binding motifs, additional predictors of variant pathogenicity and updated gene tree pipelines.

more at http://www.ensembl.info/2018/10/03/ensembl-94-is-out/

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

Rahul Nayak — Mon, 13 Nov 2017 05:10:23 -0600

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
AfterQC can simply go through all fastq files in a folder and then output three folders: good, bad and QC folders, which contains good reads, bad reads and the QC results of each fastq file/pair.
Currently it supports processing data from HiSeq 2000/2500/3000/4000, Nextseq 500/550, MiniSeq...and other Illumina 1.8 or newer formats

Address of the bookmark: https://github.com/OpenGene/AfterQC

MinION_GC: An R script to do some QC on MinION data

Radha Agarkar — Sun, 03 Dec 2017 15:19:18 -0600

Other tools focus on getting data out of the fastq or fast5 files, which is slow and computationally intensive. The benefit of this approach is that it works on a single, small, .txt summary file. So it's a lot quicker than most other things out there: it takes about a minute to analyse a 4GB flowcell on my laptop.

https://github.com/roblanf/minion_qc

Address of the bookmark: https://github.com/roblanf/minion_qc

MIX: Combining multiple assemblies from NGS data

Rahul Nayak — Tue, 08 May 2018 04:58:05 -0500

Mix is a tool that combines two or more draft assemblies, without relying on a reference genome and has the goal to reduce contig fragmentation and thus speed-up genome finishing. The proposed algorithm builds an extension graph where vertices represent extremities of contigs and edges represent existing alignments between these extremities. These alignment edges are used for contig extension. The resulting output assembly corresponds to a path in the extension graph that maximizes the cumulative contig length.

The Mix algorithm, approach and results were published in BMC bioinformatics : http://www.biomedcentral.com/1471-2105/14/S15/S16.

Address of the bookmark: https://github.com/cbib/MIX

NextSV: a meta-caller for structural variants from low-coverage long-read sequencing data

Jit — Mon, 06 Aug 2018 17:24:53 -0500

NextSV, a meta SV caller and a computational pipeline to perform SV calling from low coverage long-read sequencing data. NextSV integrates three aligners and three SV callers and generates two integrated call sets (sensitive/stringent) for different analysis purpose. The output of NextSV is in ANNOVAR-compatible bed format. Users can easily perform downstream annotation using ANNOVAR and disease gene discovery using Phenolyzer.

Address of the bookmark: https://github.com/Nextomics/NextSV

BamView: a free interactive display of read alignments in BAM data files

Neel — Fri, 09 Nov 2018 13:43:22 -0600

To run the application on UNIX from the downloaded jar file run the UNIX:

java -mx512m -jar BamView.jar

and extra command line options are given when '-h' is used:

java -jar BamView.jar -h

BAM files can be specified on the command line with the '-a' option:

java -mx512m -jar BamView.jar -a pathToFile/sorted.bam

If a BAM filename is not given on the command line BamView will prompt for a file to be entered. The BAM index file should have the same name as the BAM file but with a '.bai' suffix. Multiple BAM files can be loaded and overlaid in the viewer. To make this easier BamView will read in files that contain a list of filenames.

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

ZENBU: a collaborative, omics data integration and interactive visualization system

BioJoker — Fri, 04 Jan 2019 13:35:26 -0600

ZENBU is a data integration, data analysis, and visualization system enhanced for RNAseq, ChipSeq, CAGE and other types of next-generation-sequence-tag (NGS) based data. ZENBU allows for novel data exploration through "on-demand" data processing and interactive linked-visualizations and is able to make many-views from the same primary sequence alignment data which users can uploaded from BAM, BED, GFF and tab-text files.
Please check our documentation wiki for details on how to use the system, or check out some of the views above.

Address of the bookmark: http://fantom.gsc.riken.jp/zenbu/

OMTools: a software package for visualizing and processing optical mapping data

BioJoker — Fri, 29 Mar 2019 01:21:54 -0500

OMTools, an efficient and intuitive data processing and visualization suite to handle and explore large-scale optical mapping profiles. OMTools includes modules for visualization (OMView), data processing and simulation. These modules together form an accessible and convenient pipeline for optical mapping analyses.

https://github.com/TF-Chan-Lab/OMTools

Address of the bookmark: https://github.com/TF-Chan-Lab/OMTools