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• • LEGE@lege

  

  LEGE bookmarked dna2bit: an ultra-fast and accurate genomic distance estimation software 422 days ago

  dna2bit is a software tool developed in C++11, leveraging the capabilities of OpenMP for parallel computing and the popcount technique for efficient bit manipulation. It has been thoroughly tested using the g++ and clang compilers on both Linux and...

  https://github.com/lijuzeng/dna2bit
• • LEGE@lege

  

  LEGE bookmarked GrAnnoT 422 days ago

  GrAnnoT is an annotation transfer tool for pangenome graphs. It can transfer linear genome annotations to a pangenome graph containing the genome, and also transfer the pangenome graph's annotations on the genomes it contains. It also outputs...

  https://forge.ird.fr/diade/dynadiv/grannot
• • BioStar@biostar

  

  BioStar bookmarked GFAffix : Identifies walk-preserving shared affixes in variation graphs and collapses them into a... 425 days ago

  GFAffix identifies walk-preserving shared affixes in variation graphs and collapses them into a non-redundant graph structure.  

  https://github.com/codialab/GFAffix
• • BioStar@biostar

  

  BioStar bookmarked AlfaPang: alignment free algorithm for pangenome graph construction 425 days ago

  AlfaPang constructs variation graphs, leveraging its alignment-free and reference-free approach, based solely on intrinsic sequence properties. This design allows AlfaPang's runtime and memory usage to scale linearly with the size of input...

  https://github.com/AdamCicherski/AlfaPang
• • BioStar@biostar

  

  BioStar bookmarked Firecrawl: The Web Data API for AI - Turn entire websites into LLM-ready markdown or structured data 425 days ago

  Firecrawl is an API service that takes a URL, crawls it, and converts it into clean markdown or structured data. We crawl all accessible subpages and give you clean data for each. No sitemap required. Check out our documentation. Pst....

  https://github.com/firecrawl/firecrawl
• • BioStar@biostar

  

  BioStar bookmarked FANTASIA 433 days ago

  FANTASIA is an advanced pipeline for the automatic functional annotation of protein sequences using state-of-the-art protein language models. It integrates deep learning embeddings and in-memory similarity searches, retrieving reference vectors from...

  https://github.com/CBBIO/FANTASIA
• • Neel@neelam

  

  Neel bookmarked Jaeger : an accurate and fast deep-learning tool to detect bacteriophage sequences 439 days ago

  Jaeger is a tool that utilizes homology-free machine learning to identify phage genome sequences that are hidden within metagenomes. It is capable of detecting both phages and prophages within metagenomic assemblies. The performance of the Jaeger...

  https://github.com/MGXlab/Jaeger
• • Neel@neelam

  

  Neel bookmarked dna2bit: an ultra-fast and accurate genomic distance estimation software 439 days ago

  dna2bit: an ultra-fast and accurate genomic distance estimation software dna2bit is a software tool developed in C++11, leveraging the capabilities of OpenMP for parallel computing and the popcount technique for efficient bit manipulation. 

  https://github.com/lijuzeng/dna2bit
• • Neel@neelam

  

  Neel bookmarked BakRep (Denglish blend of Bakterien & Repository) simplifies access to this data 440 days ago

  2,438,386 bacterial genomes at your fingertips consistently processed & characterized, enriched with metadata, accessible via a flexible search engine. BakRep (Denglish blend of Bakterien & Repository) simplifies access to this data. It...

  https://bakrep.computational.bio/
• • Neel@neelam

  

  Neel published a blog post 10 Books to Kickstart (and Level Up) Your Bioinformatics Journey 441 days ago

  If you’re starting out in bioinformatics or looking to sharpen your computational biology skills, having the right learning resources makes all the difference. Here’s my curated list of 10 must-read books — from beginner-friendly introductions to...
• • Abhi@abhinav

  

  Abhi published a blog post SNP Analysis: Unlocking the Secrets in Our DNA 468 days ago

  Single Nucleotide Polymorphisms (SNPs) are the most common type of genetic variation in humans—and many other organisms. A single base change in the DNA sequence (for example, an A instead of a G) can influence everything from our eye color to...
• • Abhi@abhinav

  

  Abhi published a blog post P-Value, FDR, q-score: What Do They Mean? A Simple Guide with Example 487 days ago

  In statistics and bioinformatics, you’ll often see results reported with p-values, FDR, and q-values (q-scores). But what do these terms mean, and how are they different? Let’s break them down with simple definitions and a step-by-step example.
• • Abhi@abhinav

  

  Abhi posted to the wire 492 days ago

  Convert #GFF2BED (base) [b@hn1 DUMP]$ awk 'BEGIN {OFS = "\t"};$3=="gene"{print $1,$4-1,$5}' genomic.gff > genes.bed
• • Abhi@abhinav

  

  Abhi published a blog post What is Data Science? — A Bioinformatics Perspective 498 days ago

  In today’s era of big biology, we’re generating more data than ever before—genomes, transcriptomes, proteomes, metabolomes, microbiomes… you name it. But raw biological data doesn’t speak for itself. Making sense of it requires more than...
• • LEGE@lege

  

  LEGE published a blog post Trust But Verify: Sequencing Your Cell Lines Might Reveal an Uninvited Guest 510 days ago

  High-throughput sequencing has become indispensable in cell biology, enabling detailed insights into chromatin structure, gene expression, and regulatory dynamics. Yet, when faced with unexpectedly low mapping rates to the human genome,...
• • LEGE@lege

  

  LEGE published a fun post A Bioinformatician’s Lament 516 days ago

  "I have a presentation tomorrow," they say, With hopeful eyes, like it’s all child's play. As if results bloom overnight, full-grown— Not wrangled from chaos, and error-prone.
• • LEGE@lege

  

  LEGE published a blog post Basics of DESeq2: Differential Expression Made Simple 517 days ago

  DESeq2 is a powerful and widely-used R package that identifies differentially expressed genes (DEGs) from RNA-seq data. Whether you're comparing treated vs untreated samples, disease vs healthy conditions, or wild-type vs mutant strains, DESeq2...
• • LEGE@lege

  

  LEGE published a blog post Magic Wormhole: The Easiest Way to Send Files Securely 517 days ago

  In a world increasingly dependent on digital data exchange, secure and user-friendly file transfer solutions are more important than ever. Enter Magic Wormhole, a deceptively simple yet powerful tool that makes it trivial to send files and...
• • LEGE@lege

  

  LEGE published a blog post Unlocking Evolutionary Secrets: A Dive into Comparative Genomics Methods 525 days ago

  Comparative genomics is the art and science of comparing genomes—across species, within species, or even among individuals—to unravel evolutionary relationships, functional elements, and genetic adaptations. As sequencing technologies have...
• • BioStar@biostar

  

  BioStar published a blog post HiBC: Human Intestinal Bacteria Collection 538 days ago

  The human gut is home to trillions of microorganisms, forming one of the most complex and dynamic microbial ecosystems known to science. The Human Intestinal Bacteria Collection (HiBC) is a pioneering initiative aimed at cataloging, preserving,...

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