BOL: All site bookmarks

quarTeT: a telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification.

Abhi — Sat, 08 Jun 2024 15:54:36 -0500

quarTeT is a collection of tools for T2T genome assembly and basic analysis in automatic workflow.

Task include:

AssemblyMapper : reference-guided genome assembly
GapFiller : long-reads based gap filling
TeloExplorer : telomere identification
CentroMiner : centromere candidate prediction

https://academic.oup.com/hr/article/10/8/uhad127/7197191?login=false

Address of the bookmark: http://www.atcgn.com:8080/quarTeT/home.html

AMR Database !

LEGE — Tue, 04 Jun 2024 13:37:21 -0500

ARG-ANNOT. PMID: 24145532
CARD. PMID: 23650175
MEGARes PMID: 27899569
NCBI BioProject: PRJNA313047
plasmidfinder PMID: 24777092
resfinder. PMID: 22782487
VFDB. PMID: 26578559
SRST2's version of ARG-ANNOT. PMID: 25422674.
VirulenceFinder PMID: 24574290.

Address of the bookmark: https://github.com/sanger-pathogens/ariba/wiki/Task%3A-getref

Seeing Theory and Learn

LEGE — Tue, 04 Jun 2024 00:31:54 -0500

Seeing Theory was created by Daniel Kunin while an undergraduate at Brown University. The goal of this website is to make statistics more accessible through interactive visualizations (designed using Mike Bostock’s JavaScript library D3.js).

Address of the bookmark: https://seeing-theory.brown.edu/

Powerful books for learning data analysis with R

LEGE — Tue, 28 May 2024 07:42:56 -0500

R is powerful tool for data analysis, visualization, and machine learning. And it costs $0 to use! Here are six FREE books you can use to learn R today:

https://csgillespie.github.io/efficientR/

https://r-graphics.org/

https://rstudio-education.github.io/hopr/

https://r-pkgs.org/

https://r4ds.had.co.nz/

Address of the bookmark: https://r-graphics.org/

Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes

Abhi — Wed, 15 May 2024 14:36:12 -0500

Bactopia is a flexible pipeline for complete analysis of bacterial genomes. The goal of Bactopia is to process your data with a broad set of tools, so that you can get to the fun part of analyses quicker!

Bactopia can be split into two main parts: Bactopia Analysis Pipeline, and Bactopia Tools.

Bactopia Analysis Pipeline is the main per-isolate workflow in Bactopia. Built with Nextflow, input FASTQs (local or available from SRA/ENA) are put through numerous analyses including: quality control, assembly, annotation, minmer sketch queries, sequence typing, and more.

Bactopia Tools are a set a independent workflows fo

Address of the bookmark: https://github.com/bactopia/bactopia

The ATCC Genome Portal

Abhi — Wed, 15 May 2024 14:24:16 -0500

The ATCC Genome Portal (AGP, https://genomes.atcc.org/) is a database of authenticated genomes for bacteria, fungi, protists, and viruses held in ATCC’s biorepository. It now includes 3,938 assemblies (253% increase) produced under ISO 9000 by ATCC. Here, we present new features and content added to the AGP for the research community.

Address of the bookmark: https://genomes.atcc.org/

ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data

LEGE — Wed, 08 May 2024 07:32:45 -0500

ContigExtender, was developed to extend contigs, complementing de novo assembly. ContigExtender employs a novel recursive Overlap Layout Candidates (r-OLC) strategy that explores multiple extending paths to achieve longer and highly accurate contigs. ContigExtender is effective for extending contigs significantly in in silico synthesized and real metagenomics datasets.

More at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7953547/

Address of the bookmark: https://github.com/dengzac/contig-extender

Alvis: a tool for contig and read ALignment VISualisation and chimera detection

LEGE — Wed, 08 May 2024 07:02:55 -0500

Alvis, a simple command line tool that can generate visualisations for a number of common alignment analysis tasks. Alvis is a fast and portable tool that accepts input in a variety of alignment formats and will output production ready vector images. Additionally, Alvis will highlight potentially chimeric reads or contigs, a common source of misassemblies.

More at https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04056-0

Address of the bookmark: https://github.com/SR-Martin/alvis

Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes

LEGE — Mon, 06 May 2024 06:21:10 -0500

Genomic regulatory blocks are chromosomal regions spanned by long clusters of highly conserved noncoding elements devoted to long-range regulation of developmental genes, often immobilizing other, unrelated genes into long-lasting syntenic arrangements. Synorth http://synorth.genereg.net/ is a web resource for exploring and categorizing the syntenic relationships in genomic regulatory blocks across multiple genomes, tracing their evolutionary fate after teleost whole genome duplication at the level of genomic regulatory block loci, individual genes, and their phylogenetic context.

More at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2745767/

Address of the bookmark: http://synorth.genereg.net/

Virus Bioinformatics Tools

LEGE — Wed, 24 Apr 2024 06:19:55 -0500

Bioinformatics tools play a crucial role in studying viruses, enabling researchers to analyze their genetic makeup, structure, function, and evolution. Here are some commonly used bioinformatics tools for virus research

https://evirusbioinfc.notion.site/18e21bc49827484b8a2f84463cb40b8d?v=92e7eb6703be4720abf17a901bc9a947

Address of the bookmark: https://evirusbioinfc.notion.site/18e21bc49827484b8a2f84463cb40b8d?v=92e7eb6703be4720abf17a901bc9a947