BOL: Related items

CONTIGuator !

BioStar — Fri, 04 Oct 2019 01:27:58 -0500

CONTIGuator is a Python script for Linux environments whose purpose is to speed-up the bacterial genome assembly process and to obtain a first insight of the genome structure using the well-known artemis comparison tool (ACT).

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

Shinyheatmap

Jit — Fri, 21 Oct 2016 05:12:11 -0500

Background: Transcriptomics, metabolomics, metagenomics, and other various next-generation sequencing (-omics) fields are known for their production of large datasets. Visualizing such big data has posed technical challenges in biology, both in terms of available computational resources as well as programming acumen. Since heatmaps are used to depict high-dimensional numerical data as a colored grid of cells, efficiency and speed have often proven to be critical considerations in the process of successfully converting data into graphics. For example, rendering interactive heatmaps from large input datasets (e.g., 100k+ rows) has been computationally infeasible on both desktop computers and web browsers. In addition to memory requirements, programming skills and knowledge have frequently been barriers-to-entry for creating highly customizable heatmaps. Results: We propose shinyheatmap: an advanced user-friendly heatmap software suite capable of efficiently creating highly customizable static and interactive biological heatmaps in a web browser. shinyheatmap is a low memory footprint program, making it particularly well-suited for the interactive visualization of extremely large datasets that cannot typically be computed in-memory due to size restrictions. Conclusions: shinyheatmap is hosted online as a freely available web server with an intuitive graphical user interface: http://shinyheatmap.com. The methods are implemented in R, and are available as part of the shinyheatmap project at: https://github.com/Bohdan-Khomtchouk/shinyheatmap.

More at http://biorxiv.org/content/early/2016/09/21/076463

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

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

IMPUTE2

Jit — Thu, 27 Oct 2016 11:21:44 -0500

IMPUTE2 is a computer program for phasing observed genotypes and imputing missing genotypes. Most people use just a couple of the program's basic functions, but we have also built up a collection of specialized and powerful options. If you are new to IMPUTE2, or indeed to phasing and imputation in general, we suggest that you start by learning the basics.

You should begin by downloading the program from here. You will need to choose the link that matches your computing platform and then follow the instructions for opening the download package.

Once you have done this, you will be ready to try some example analyses on the test data that are provided with the download. The section on Examples shows how to use the most common IMPUTE2 functions. We suggest that you work through these examples and try to understand what the elements of each command are doing. If you don't understand something or would like to know if the program can perform a function that isn't listed, you can read our FAQ or submit a question to our mail list.

When you have learned the basic functionality of the program, you can use several features of this website to prepare your own analysis:

Learn about best practices for imputation.
Download reference data that you can use to impute genotypes in your study.
Look through a complete list of program options.

Address of the bookmark: https://mathgen.stats.ox.ac.uk/impute/impute_v2.html

Biological databases !

BioStar — Wed, 12 Feb 2020 01:16:29 -0600

Now a days there are a lots of genomics databases available around the world. This bookmark is created to provide all links in one place ...

ftp://ftp.ncbi.nih.gov/genomes/

https://hgdownload.soe.ucsc.edu/downloads.html

Address of the bookmark: ftp://ftp.ncbi.nih.gov/genomes/

Research Associate and Junior Research Fellow at North-Eastern Hill University - Tura, Meghalaya

Fri, 28 Oct 2016 09:54:43 -0500

Research Associate and Junior Research Fellow
North-Eastern Hill University - Tura, Meghalaya
₹18,000 a month
Applications are invited for the post of Research Associate and JRF in the DBT sponsored Bioinformatics Infrastructure Facility (BIF), posts are purely temporary and terminable at anytime without prior notice or assigning any reason thereof.

Research Associate :
Essential Qualification: Ph.D in Bioinformatics/Biotechnology/Life Science from a reocngised univeristy/institute
Pay: Rs.36000-/- + Admissible 10% HRA per month
Age: Below 35 years

Junior Research Fellow
Essential Qualification: M.Sc in Bioinformatics/Biotechnology/Life Science from a reocngised univeristy/institute
Pay: Rs.18000-/- + per month
Age: Below 35 years

Last date for receving application by mail or post is 08.11.2016

Company Info.
North-Eastern Hill University

Bioinformatics Infrastructure Facility (BIF) Department of RDAP North-Eastern Hill University, Tura Campus Tura-794002, Meghalaya

More at http://www.nehu.ac.in/Advertisements/BIFTuraManpowerAdvt_25102016.pdf

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

HybPiper

Jit — Fri, 04 Nov 2016 05:02:10 -0500

HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads.

Targeted bait capture is a technique for sequencing many loci simultaneously based on bait sequences. HybPiper pipeline starts with high-throughput sequencing reads (for example from Illumina MiSeq), and assigns them to target genes using BLASTx or BWA. The reads are distributed to separate directories, where they are assembled separately using SPAdes. The main output is a FASTA file of the (in frame) CDS portion of the sample for each target region, and a separate file with the translated protein sequence.

HybPiper also includes post-processing scripts, run after the main pipeline, to also extract the intronic regions flanking each exon, investigate putative paralogs, and calculate sequencing depth. For more information, please see our wiki.

HybPiper is run separately for each sample (single or paired-end sequence reads). When HybPiper generates sequence files from the reads, it does so in a standardized directory hierarchy. Many of the post-processing scripts rely on this directory hierarchy, so do not modify it after running the initial pipeline. It is a good idea to run the pipeline for each sample from the same directory. You will end up with one directory per run of HybPiper, and some of the later scripts take advantage of this predictable directory structure.

Address of the bookmark: https://github.com/mossmatters/HybPiper

Sample bandage input file for visual analysis

Jit — Wed, 06 Jan 2021 03:51:50 -0600

Sample bandage input file for visual analysis ...

R Graphical Cookbook by Winston Chang

Abhimanyu Singh — Fri, 04 Nov 2016 12:50:30 -0500

R Graphical Cookbook by Winston Chang

A very nice book by Winston Chang for R ethusiast. The R code presented in these pages is the R code actually used to produce the Figures in the book. There will be differences compared to the code chunks shown in the text of the book, but in most cases the differences will be that these pages contain additional code to lay out multiple plots on a single "page".

The code presented for each figure is self-contained, i.e., all code required to produce the figure is included. This means that there is sometimes considerable overlap of code between several figures In some cases, it may be necessary to install an add-on package from CRAN to get the code to run.

More books at http://www.e-reading.club/bookreader.php/137370/C486x_APPb.pdf