BOL

UnCoVar: Workflow for Transparent and Robust Virus Variant Calling, Genome Reconstruction and Lineage Assignment Using state of the art tools, easily extended for other viruses Tool and database updates for critical components via...

Meta-transcriptomics combines high-throughput sequencing technologies with computational biology to profile the RNA content of a sample.

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...

Variant Calling - Resequencing-Based Genome Inference Erik GarrisonUniversity of Tennessee Health Science CenterWorkshop on Genomics - Český KrumlovJanuary 12,...

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...

1. Ktrim: An extra-fast, accurate adapter trimmer for sequencing data. It processes FASTQ files from multiple lanes with minimal mismatching and over-trimming of adapters.2. BWA MEM: A reliable alignment tool (particularly for mapping ALT contigs...

The Basic Local Alignment Search Tool (BLAST) is a powerful bioinformatics program used to compare an input sequence (such as DNA, RNA, or protein sequences) against a database of sequences to find regions of similarity.

A while ago we posted a request for online resources on must-read papers in evolutionary biology, for a literature club. We received many answers in the meantime

https://ncbiinsights.ncbi.nlm.nih.gov/2024/07/15/refseq-release-225/

To block a node  srun --partition=compute --nodes=1 --ntasks-per-node=40 --pty bash.sh

Welcome to the course notes for STAT 414: Introduction to Probability Theory. These notes are designed and developed by Penn State's Department of Statistics and offered as open educational resources. These notes are free to use under...

The Protist 10,000 Genomes (P10K) Project aims to decipher the genome sequences and construct a comprehensive database resource containing over 10,000 species of protists, encompassing representatives from every major clade. Samples were collected...

iMAGine is a metagenomic workflow which includes filtering, assembling, and binning. This workflow includes the following tools which are needed to be installed in the system. fastp spades assembler QUAST bwa samtools metabat2 CheckM

SqueezeMeta is a full automatic pipeline for metagenomics/metatranscriptomics, covering all steps of the analysis. SqueezeMeta includes multi-metagenome support allowing the co-assembly of related metagenomes and the retrieval of individual genomes...

Created by Stephen Johnson, Brett Trost, Dr. Jeffrey R. Long, Dr. Anthony Kusalik University of Saskatchewan, Department of Computer Science BEAR is intended to be an easy-to-use collection of scripts for generating simulated WGS metagenomic reads...

YAMP is constructed on Nextflow, a framework based on the dataflow programming model, which allows writing workflows that are highly parallel, easily portable (including on distributed systems), and very flexible and customisable,...

sourmash is a k-mer analysis multitool, and we aim to provide stable, robust programmatic and command-line APIs for a variety of sequence comparisons. Some of our special sauce includes: FracMinHash sketching, which enables accurate...

Lorikeet is a within-species variant analysis pipeline for metagenomic communities that utilizes both long and short reads. Lorikeet utilizes a re-implementaion of the GATK HaplotypeCaller algorithm, performing local re-assembly of potentially...

DRAM (Distilled and Refined Annotation of Metabolism) is a tool for annotating metagenomic assembled genomes and VirSorter identified viral contigs. DRAM annotates MAGs and viral contigs using KEGG (if provided by the...

Interesting plots https://www.machinelearningplus.com/plots/top-50-matplotlib-visualizations-the-master-plots-python/ #Plots #Idea