BOL: Related items

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

nf-core/mag v5: Advancing Genome-Resolved Metagenomics

LEGE — Sat, 12 Sep 2026 20:27:51 -0500

Metagenomics is rapidly moving beyond short-read sequencing. With the increasing adoption of long-read technologies, researchers can generate more contiguous assemblies—but converting these reads into reliable metagenome-assembled genomes (MAGs) remains computationally challenging.

nf-core/mag v5 (https://github.com/nf-core/mag) addresses this challenge by extending its reproducible Nextflow-based workflow for modern genome-resolved metagenomics.

A key addition is support for long-read-only metagenomic assembly and bin refinement, enabling long-read data to be processed through an integrated workflow. The release also introduces five additional binning tools, providing complementary strategies for recovering genomes from complex microbial communities.

The workflow has also expanded beyond conventional bacterial and archaeal MAGs, with improved classification of viruses and eukaryotes, together with enhanced genome-quality assessment.

Conceptually, the workflow brings together:

Reads → QC → Assembly → Binning → Bin refinement → Taxonomic classification → MAG quality assessment

The real strength of nf-core/mag is not any single algorithm, but the integration and reproducibility of multiple tools within a standardized workflow. This is particularly important for large-scale metagenomic studies where software versions, parameters, databases and computational environments can strongly influence results.

After seven years of development involving multiple curator teams and the wider nf-core community, v5 demonstrates how community-driven workflow development can keep metagenomic analysis aligned with rapidly evolving sequencing technologies.

The future of genome-resolved metagenomics is not simply longer reads—it is better integration of assembly, binning, refinement and quality control within reproducible computational workflows.

Read the full paper in Bioinformatics https://academic.oup.com/bioinformatics/article/42/9/btag628/8770536?

Claus-Peter Stelzer Lab

Mon, 15 Mar 2021 15:24:41 -0500

Interested in various topics at the intersection of ecology and evolution. In my research I use rotifers as model organisms for experimental studies at the individual and population level. Rotifers are ideally suited for this, because populations of thousands can be kept in small containers in the lab, while single individuals can still be handled conveniently.

More at https://www.uibk.ac.at/limno/personnel/stelzer/index.html.en#research

Genome + Epigenome = New Understanding of the Pathogens in Your Food

Fri, 27 Sep 2013 11:30:45 -0500

UC Davis's Bart Weimer describes foodborne pathogens and their proclivity for rapid genome rearrangement. The 100K Pathogen Genome Project he leads is using PacBio long-read sequencing to close genomes and analyze methylation; Weimer reports that his team has already discovered new epigenetic modifications in Salmonella and Listeria with the technology. www.pacb.com/microbe

Bioinformatician duties and jobs !!!

Jitendra Narayan — Wed, 05 Mar 2014 14:32:26 -0600

Needle in a haystack ... ohh yes this is what bioinformatician do. We handle and analyse, Terabytes and Petabytes of genomic data on daily basis.

Nieduszynski Group

Fri, 26 Sep 2014 19:35:06 -0500

Complete, accurate replication of the genome is essential for life. All chromosomes in eukaryotic cells must be duplicated and then segregated to daughter cells to ensure genetic integrity and produce the large number of cells that make up a multicellular organism. We are using genetic, genomic and computational methods to understand how chromosome replication is regulated to ensure genome stability. By focusing on the basic biology that underpins cell growth and division we aim to provide new insights that may help our understanding of diseases such as cancer and congenital disorders.

More http://www.nieduszynski.org/index.php
http://www.path.ox.ac.uk/research/cell-biology-and-pathology/conrad-nieduszynski-group

ShRec3D

Jitendra Narayan — Thu, 25 Dec 2014 23:14:52 -0600

ShRec3D is a program that aims at reconstructing a genome 3D structure (b) from the sole knowledge of the contacts between different genomic regions (a) as determined by Hi-C (http://www.ncbi.nlm.nih.gov/pubmed/19815776).

There are two options to run ShRec3D (on linuX only so far): the first one uses the Matlab complier runtime environment (MCR), the second one doesn't need any other library to be installed but only works with the latest versions of Linux (equivalent to Fedora 19 and above).

Address of the bookmark: https://sites.google.com/site/julienmozziconacci/#TOC-Downloads

Sequencing By Xpansion

Jitendra Narayan — Wed, 17 Jun 2015 20:58:11 -0500

Sequencing By Xpansion (SBX) is a DNA sequencing method that uses a simple biochemical reaction to encode the sequence of a DNA molecule into a highly measurable surrogate called an Xpandomer. This single molecule approach produces enough Xpandomer in a single drop reaction to sequence an entire human genome 1000X over. To achieve this, an Xpandomer replaces each DNA sequence with a sequence of large, high signal reporter molecules using the SBX molecular expansion technology. The DNA sequence is then read out as the Xpandomer reporters pass sequentially through a nanopore detector. SBX is a molecular engineering platform that benefits from core design principles that separate the multiple molecular functions. This systems approach enables efficient development and incorporation of improvements to SBX and is key to reconfiguring and optimizing Xpandomer measurement for different detection platforms.

http://www.stratosgenomics.com/stratos-genomics-technology

Ensembl comparative genomics resources

Jitendra Narayan — Sun, 28 Feb 2016 17:10:20 -0600

The Ensembl comparative genomics resources are one such reference set that facilitates comprehensive and reproducible analysis of chordate genome data. Ensembl computes pairwise and multiple whole-genome alignments from which large-scale synteny, per-base conservation scores and constrained elements are obtained. Gene alignments are used to define Ensembl Protein Families, GeneTrees and homologies for both protein-coding and non-coding RNA genes. These resources are updated frequently and have a consistent informatics infrastructure and data presentation across all supported species. Specialized web-based visualizations are also available including synteny displays, collapsible gene tree plots, a gene family locator and different alignment views. The Ensembl comparative genomics infrastructure is extensively reused for the analysis of non-vertebrate species by other projects including Ensembl Genomes and Gramene and much of the information here is relevant to these projects. The consistency of the annotation across species and the focus on vertebrates makes Ensembl an ideal system to perform and support vertebrate comparative genomic analyses. We use robust software and pipelines to produce reference comparative data and make it freely available.

Database URL: http://www.ensembl.org.

Address of the bookmark: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4761110/

RATT

Jitendra Narayan — Sun, 07 Feb 2016 16:09:40 -0600

RATT is software to transfer annotation from a reference (annotated) genome to an unannotated query genome.

It was first developed to transfer annotations between different genome assembly versions. However, it can also transfer annotations between strains and even different species, like Plasmodium chabaudi onto P. berghei, between different Leishmania species or Salmonella enterica onto other Salmonella serotypes. RATT is able to transfer any entries present on a reference sequence, such as the systematic id or an annotator's notes; such information would be lost in a de novo annotation.

More at http://ratt.sourceforge.net/

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