BOL: Related items

JBrowse: Embeddable genome browser built completely with JavaScript and HTML5

Jit — Fri, 29 Jun 2018 09:19:56 -0500

JBrowse is a fast, embeddable genome browser built completely with JavaScript and HTML5, with optional run-once data formatting tools written in Perl. Headline Features: Fast, smooth scrolling and zooming. Explore your genome with unparalleled speed. Scales easily to multi-gigabase genomes and deep-coverage sequencing. Quickly open and view data files on your computer without uploading them to any server. Supports GFF3, BED, FASTA, Wiggle, BigWig, BAM, VCF (with either .tbi or .idx index), REST, and more. BAM, BigBed, BigWig, and VCF data are displayed directly from chunks of the compressed binary files, no conversion needed. Includes an optional “faceted” track selector (see demo) suitable for large installations with thousands of tracks. Very light server resource requirements. In fact, JBrowse has no back-end server code, just tools for formatting data files to be read directly over HTTP. Serve huge datasets from a single low-cost cloud instance. Can run as a stand-alone app on OSX and Windows using the Electron platform Highly extensible plugin architecture, with a large plugin registry of existing examples here https://gmod.github.io/jbrowse-registry https://jbrowse.org/

Address of the bookmark: https://github.com/GMOD/jbrowse

LR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly

Rahul Nayak — Thu, 14 May 2020 15:09:52 -0500

LR_Gapcloser is a gap closing tool using long reads from studied species. The long reads could be downloaed from public read archive database (for instance, NCBI SRA database ) or be your own data. Then they are fragmented and aligned to scaffolds using BWA mem algorithm in BWA package. In the package, we provided a compiled bwa, so the user needn't to install bwa. LR_Gapcloser uses the alignments to find the bridging that cross the gap, and then fills the long read original sequence into the genomic gaps.

Address of the bookmark: https://github.com/CAFS-bioinformatics/LR_Gapcloser

Long read assembly workshop !

Rahul Nayak — Thu, 04 Oct 2018 17:23:18 -0500

This is a tutorial for a workshop on long-read (PacBio) genome assembly.

It demonstrates how to use long PacBio sequencing reads to assemble a bacterial genome, and includes additional steps for circularising, trimming, finding plasmids, and correcting the assembly with short-read Illumina data.

Please comment if you know any other long read addembly tutorial.

Address of the bookmark: http://sepsis-omics.github.io/tutorials/modules/cmdline_assembly_v2/

Genobuntu: A software package containing more than 70 software and packages oriented towards NGS and genome assembly

BioStar — Tue, 11 Dec 2018 05:15:57 -0600

Genobuntu is a software package containing more than 70 software and packages oriented towards NGS. In its current version, Genobuntu supports pre assembly tools, genome assemblers as well as post assembly tools.

Commonly used biological software and example script files for different assembly pipelines have also been provided, where the example script files can be updated to suit one’s experimental needs. Genobuntu attempts to reduce the amount of time and energy needed to build software workstations and it can also act as a good teaching source for a class room setting.

https://sourceforge.net/projects/genobuntu/

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

Cogent: a tool for reconstructing the coding genome using high-quality full-length transcriptome sequences.

Jit — Tue, 18 Jun 2019 05:33:04 -0500

Cogent is a tool that identifies gene families and reconstructs the coding genome using high-quality transcriptome data without a reference genome, and can be used to check assemblies for the presence of these known coding sequences.

Cogent is a tool for reconstructing the coding genome using high-quality full-length transcriptome sequences. It is designed to be used on Iso-Seq data and in cases where there is no reference genome or the ref genome is highly incomplete.

See a recent presentation on Cogent being applied to the Cuttlefish Iso-Seq data.

Cogent preliminary draft paper (updated 2016Dec version), Supplementary

Please see wiki for details on usage.

Address of the bookmark: https://github.com/Magdoll/Cogent

AirLift, a methodology and tool for comprehensively moving mappings and annotations from one genome to another similar genome

Jit — Mon, 23 Dec 2019 10:20:13 -0600

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

HASLR: a tool for rapid genome assembly of long sequencing reads

LEGE — Fri, 31 Jan 2020 05:50:15 -0600

HASLR is a tool for rapid genome assembly of long sequencing reads. HASLR is a hybrid tool which means it requires long reads generated by Third Generation Sequencing technologies (such as PacBio or Oxford Nanopore) together with Next Generation Sequencing reads (such as Illumina) from the same sample.

Address of the bookmark: https://github.com/vpc-ccg/haslr

shinyChromosome:a GUI for the interactive creation of non-circular whole genome diagrams

Jit — Sat, 29 Feb 2020 00:39:50 -0600

shinyChromosome is a graphical user interface for interactive creation of non-circular whole genome diagrams developed using the R Shiny package.

To create single-genome plot by aligning genome data along all chromosomes of a single genome, go to the Single-genome plot menu.

To cretae two-genome plot for comparison of data across two genomes, go to the Two-genome plot menu.

For the detail format of input data, check the Input data format submenu of the Help menu.

shinyChromosome is deployed at http://150.109.59.144:3838/shinyChromosome/, http://shinyChromosome.ncpgr.cn, and https://yimingyu.shinyapps.io/shinyChromosome for online use. The source code and manual of shinyChromosome are freely available at https://github.com/venyao/shinyChromosome.

https://yimingyu.shinyapps.io/shinychromosome/

https://www.sciencedirect.com/science/article/pii/S1672022919301883

Address of the bookmark: https://yimingyu.shinyapps.io/shinychromosome/

Coronavirus Resources !

Neel — Wed, 25 Mar 2020 17:11:33 -0500

2019nCoVR features comprehensive integration of genomic and proteomic sequences as well as their metadata information from the GISAID, NCBI, NMDC and CNCB/NGDC. It also incorporates a wide range of relevant information including scientific literatures, news, and popular articles for science dissemination, and provides visualization functionalities for genome variation analysis results based on all collected 2019-nCoV strains.

Annotation

https://bigd.big.ac.cn/ncov/variation/annotation

Genome wharehouse

https://bigd.big.ac.cn/gwh/browse/index

Released Genome

https://bigd.big.ac.cn/ncov/release_genome

Download data

ftp://download.big.ac.cn/Genome/Viruses/Coronaviridae/

Raw data

https://bigd.big.ac.cn/gsa/browse/run/?tag=Coronaviridae

Address of the bookmark: https://bigd.big.ac.cn/ncov/about

merqury: Evaluate genome assemblies with k-mers

Jit — Fri, 03 Jul 2020 19:29:34 -0500

Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual. The k-mer spectrum of this read set can be used for independently evaluating assembly quality without the need of a high quality reference. Merqury provides a set of tools for this purpose.

More at https://www.biorxiv.org/content/10.1101/2020.03.15.992941v1.full

Address of the bookmark: https://github.com/marbl/merqury