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• • BioStar@biostar

  

  BioStar bookmarked P10K: The Protist 10,000 Genomes 138 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 138 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 138 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 138 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 138 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. 138 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 138 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 138 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 154 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 156 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 159 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 159 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
• • Neel@neelam

  

  Neel bookmarked SeqCAT: Sequence Conversion and Analysis Toolbox 159 days ago

  Your all-in-one solution for smooth conversion of sequence coordinates. Designed for bioinformatics data analysis and daily laboratory work, SeqCAT simplifies sequence coordinate conversion. Extract gene and transcript information, manipulate...

  https://mtb.bioinf.med.uni-goettingen.de/SeqCAT/home
• • Abhi@abhinav

  

  Abhi created a new bio-script Python script to parse a FASTQ file ! 164 days ago
• • Abhi@abhinav

  

  Abhi created a new bio-script Python script to calculate basic genome stats ! 164 days ago
• • Abhi@abhinav

  

  Abhi created a new bio-script Python script to create fastq file with random sequences 164 days ago
• • Abhi@abhinav

  

  Abhi bookmarked Bactopia: a flexible pipeline for complete analysis of bacterial genomes 165 days ago

  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...

  https://bactopia.github.io/latest/
• • Abhi@abhinav

  

  Abhi bookmarked MetaGraph: Ultra Scalable Framework for DNA Search, Alignment, Assembly 165 days ago

  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,...

  https://metagraph.ethz.ch/
• • Abhi@abhinav

  

  Abhi bookmarked Fundamentals of Data Visualization by Claus O. Wilke 165 days ago

  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...

  https://clauswilke.com/dataviz/
• • Abhi@abhinav

  

  Abhi bookmarked ULTRA (ULTRA Locates Tandemly Repetitive Areas) : Effective Labeling of Repetitive Genomic Sequence 165 days ago

  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...

  https://github.com/TravisWheelerLab/ULTRA

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