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• • Abhi@abhinav

  

  Abhi bookmarked Variant Calling Resequencing-Based Genome Inference 147 days ago

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

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

  

  Abhi bookmarked DIY Transcriptomics 147 days ago

  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...

  https://diytranscriptomics.com
• • BioStar@biostar

  

  BioStar created a page Important Bioinformatics Tools ! 148 days ago

  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...
• • BioStar@biostar

  

  BioStar published a blog post Basics of BLAST Programs ! 152 days ago

  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.
• • BioStar@biostar

  

  BioStar published a blog post Online resources on must-read papers in evolutionary biology 152 days ago

  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
• • Abhi@abhinav

  

  Abhi published a news post New Release of RefSeq ! 162 days ago

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

  

  BioStar commented on a page titled Keep Your Important SSH Session Running when You Disconnect from Server !!! 170 days ago

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

  

  BioStar bookmarked Free resources to learn statistics 172 days ago

  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...

  https://online.stat.psu.edu/stat414/
• • BioStar@biostar

  

  BioStar bookmarked P10K: The Protist 10,000 Genomes 172 days ago

  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...

  https://ngdc.cncb.ac.cn/p10k/
• • BioStar@biostar

  

  BioStar bookmarked iMAGine - in silico MetAGenomics pipeline 172 days ago

  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

  https://github.com/avishekdutta14/iMAGine
• • BioStar@biostar

  

  BioStar bookmarked SqueezeMeta: a fully automated metagenomics pipeline, from reads to bins 172 days ago

  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...

  https://github.com/jtamames/SqueezeMeta
• • BioStar@biostar

  

  BioStar bookmarked BEAR: Better Emulation for Artificial Reads 172 days ago

  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...

  https://github.com/sej917/BEAR
• • BioStar@biostar

  

  BioStar bookmarked YAMP: Yet Another Metagenomic Pipeline 172 days ago

  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,...

  https://github.com/alesssia/YAMP
• • BioStar@biostar

  

  BioStar bookmarked sourmash: Quickly search, compare, and analyze genomic and metagenomic data sets. 172 days ago

  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...

  https://github.com/sourmash-bio/sourmash
• • BioStar@biostar

  

  BioStar bookmarked Lorikeet: Strain resolver for metagenomics 172 days ago

  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...

  https://github.com/rhysnewell/Lorikeet
• • BioStar@biostar

  

  BioStar bookmarked DRAM: Distilled and Refined Annotation of Metabolism 172 days ago

  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...

  https://github.com/WrightonLabCSU/DRAM
• • Neel@neelam

  

  Neel posted to the wire 188 days ago

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

  

  Neel bookmarked BioKit: a set of tools dedicated to bioinformatics, data visualisation 190 days ago

  BioKit is a set of tools dedicated to bioinformatics, data visualisation (biokit.viz), access to online biological data (e.g. UniProt, NCBI thanks to bioservices). It also contains more advanced tools related to data analysis...

  https://biokit.readthedocs.io/en/latest/index.html
• • Neel@neelam

  

  Neel posted to the wire 193 days ago

  Prompt: GPT-4, Image Creation: Midjourney, Image Resolution Improvement: Magnific, Image to Video: Luma AI, Video Upscaling: TensorPix, Sound Effect Generation: OptimizerAI, Video Editing: CapCu
• • Neel@neelam

  

  Neel bookmarked Panacus : A Counting Tool for Pangenome Graphs 193 days ago

  panacus is a tool for calculating statistics for GFA files. It supports GFA files with P and W lines, but requires that the graph is blunt, i.e., nodes do not overlap and consequently, each link (L) points...

  https://github.com/marschall-lab/panacus

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