BOL: Abhi's bookmarks

NASA Open Science Data Repository

Abhi — Wed, 18 Dec 2024 11:54:47 -0600

The NASA Open Science Data Repository (OSDR) enables access to space-related data from experiments and missions that investigate biological and health responses of terrestrial life to spaceflight. The goal of OSDR is to enable multi-modal and multi-hierarchical fundamental space life science data be reused toward basic science, applied science, and operational outcomes for space exploration and knowledge discovery. These data include ‘omics, phenotypic, physiological, behavioral, hardware, environmental telemetry; raw, processed; tabular, text, code, bioimaging, and video.

https://www.nasa.gov/reference/osdr-data-processing/

Address of the bookmark: https://www.nasa.gov/osdr/

Bioinformatics Workshops !

Abhi — Wed, 31 Jul 2024 02:16:53 -0500

When delving into bioinformatics, having access to reliable resources is crucial for effective research and analysis. Key online resources include the National Center for Biotechnology Information (NCBI), which offers tools like BLAST for sequence alignment and comprehensive gene databases. For presentations and educational materials, exploring SlideShare for introductory and advanced bioinformatics topics can provide valuable insights and learning aids.

https://evomics.org/2024-workshop-on-genomics/

Address of the bookmark: https://evomics.org/2024-workshop-on-genomics/

Variant Calling Resequencing-Based Genome Inference

Abhi — Wed, 31 Jul 2024 02:02:24 -0500

Variant Calling - Resequencing-Based Genome Inference

Erik Garrison
University of Tennessee Health Science Center
Workshop on Genomics - Český Krumlov
January 12, 2024

https://evomics.org/wp-content/uploads/2024/01/Variant-calling-Workshop-on-Genomics-2024-Cesky-Krumlov.pdf

Address of the bookmark: https://evomics.org/wp-content/uploads/2024/01/Variant-calling-Workshop-on-Genomics-2024-Cesky-Krumlov.pdf

DIY Transcriptomics

Abhi — Wed, 31 Jul 2024 01:19:26 -0500

A semester-long course covering best practices for the analysis of high-throughput sequencing data from gene expression (RNA-seq) studies, with a primary focus on empowering students to be independent in the use of lightweight and open-source software using the R programming language and the Bioconductor suite of packages. This course follows a hybrid format in which online lectures are paired with in-person labs where students participate in hands-on, live coding exercises using real ‘omic datasets. The course is focused on datasets and topics central to infectious disease research, immunology, and One-Health, but the concepts and approaches covered are applicable to any genomic study.

https://diytranscriptomics.com

Address of the bookmark: https://diytranscriptomics.com

Bactopia: a flexible pipeline for complete analysis of bacterial genomes

Abhi — Sat, 08 Jun 2024 16:25:08 -0500

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

Bactopia was inspired by Staphopia, a workflow we (Tim Read and myself) released that is targeted towards Staphylococcus aureus genomes. Using what we learned from Staphopia and user feedback, Bactopia was developed from scratch with usability, portability, and speed in mind from the start.

Bactopia uses Nextflow to manage the workflow, allowing for support of many types of environments (e.g. cluster or cloud). Bactopia allows for the usage of many public datasets as well as your own datasets to further enhance the analysis of your sequencing. Bactopia only uses software packages available from Bioconda and Conda-Forge to make installation as simple as possible for all users.

To highlight the use of Bactopia and Bactopia Tools, we performed an analysis of 1,664 public Lactobacillus genomes, focusing on Lactobacillus crispatus, a species that is a common part of the human vaginal microbiome. The results from this analysis are published in mSystems under the title: Bactopia: a flexible pipeline for complete analysis of bacterial genomes

Address of the bookmark: https://bactopia.github.io/latest/

MetaGraph: Ultra Scalable Framework for DNA Search, Alignment, Assembly

Abhi — Sat, 08 Jun 2024 16:15:25 -0500

The MetaGraph framework is designed to work with a wide range of input data sets, indexing from a few samples up to the contents of entire archives with hundreds of thousands of records. The indexing workflow always follows the same principle, transforming single input samples into error-removed, refined sample graphs, which are then merged into a joint metagraph index. Each input sample is annotated in the joint index as a subgraph. This graph index enriched with metadata can then be used for downstream applications such as sequence search or differential assembly.

Searcg link https://metagraph.ethz.ch/search

Pre-print https://www.biorxiv.org/content/10.1101/2020.10.01.322164v4

Address of the bookmark: https://metagraph.ethz.ch/

Fundamentals of Data Visualization by Claus O. Wilke

Abhi — Sat, 08 Jun 2024 16:07:19 -0500

The book is meant as a guide to making visualizations that accurately reflect the data, tell a story, and look professional. It has grown out of my experience of working with students and postdocs in my laboratory on thousands of data visualizations. Over the years, I have noticed that the same issues arise over and over. I have attempted to collect my accumulated knowledge from these interactions in the form of this book.

The entire book is written in R Markdown, using RStudio as my text editor and the bookdown package to turn a collection of markdown documents into a coherent whole. The book’s source code is hosted on GitHub, at https://github.com/clauswilke/dataviz.

Address of the bookmark: https://clauswilke.com/dataviz/

ULTRA (ULTRA Locates Tandemly Repetitive Areas) : Effective Labeling of Repetitive Genomic Sequence

Abhi — Sat, 08 Jun 2024 16:03:39 -0500

ULTRA is a tool to find and annotate tandem repeats inside genomic sequence. It is able to find repeats of any length and of any period (up to a maximum period of 4000). It can find highly decayed repeats missed by other software, and it will also be able to find very large repeats in highly repetitive sequence, regardless of the size of sequence or length of repeats. ULTRA offers meaningful annotation scores and can produce annotation P-values at user request.

More at https://www.biorxiv.org/content/10.1101/2024.06.03.597269v1

Address of the bookmark: https://github.com/TravisWheelerLab/ULTRA

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

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