Ultima Genomics’ Post

Here is a post from Marco at BioTx.ai having conducted a quick research about the cost savings and trial success rates when using bioinformatics and public genome data for therapeutic programs.

De novo genome assembly steps: Different De novo genome assemblers use different algorithms to find overlaps, arrange and merge the DNA reads into larger contiguous sequences called contigs. SPAdes and velvet are examples of assemblers that use De-Bruijn Graph algorithm which depends on breaking down the reads into smaller k-mers (sequences of k nucleotides), construct a De Bruijn graph where nodes represent k-mers and edges represent overlaps of k-1 nucleotides. What are the practical steps for genome assembly? 1- Download sequence reads: The rule is: the more data you get, the more successful the assembly is. - Short reads (illumina): Reads generated from illumina sequencing can be downloaded from SRA from NCBI. These sequences are usually present in fastq format. You can download using the command line tool (wget). After downloading, 2 files are generated in gz compressed format. One file for forward reads and the other for reverse reads as it is paired-end sequencing. - Long reads(PacBio): Reads generated from PacBio are usually long reads, enabling easier genome assembly. You can download the dataset from the website https://lnkd.in/dMiY5StP. 2- Evaluate the input reads: - Run FASTQC to view the quality scores of the sequence reads. - After that, we trim bad-quality reads using Trimmomatic. 3- Assemble the genome using minia, velvet, SPAdes or any other suitable assembler. Each assembler has its own parameters. 4- check the quality of the genome using QUAST. Note that in case there is a reference genome for the organism under study, you can compare the assembled genome to the reference genome by aligning the assembled genome against the reference genome using BWA and visualising the alignment using IGV. #Bioinformatics #genomeassembly

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Want to learn how to perform a single-cell RNA sequencing analysis from instruments to insights? Our latest webinar explores crucial techniques for each step of the process, including data handling, quality control, alignment, clustering, and visualization, offering invaluable insights for researchers in the field. Whether you're navigating diverse data types or seeking to optimize your analysis workflow, this webinar provides practical guidance to elevate your #scRNAseq research endeavors. In this brief snippet, our bioinformatics engineer Nora Kearns walks through an overview of the analysis process. Access the full recording for a comprehensive exploration of #singlecell analysis techniques: https://lnkd.in/guTEsguX #bioinformatictools #singlecell #sequencinganalysis

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Pathway or gene set enrichment analysis is frequently used in genomic studies. Make sure you understand it with these 8 resources:🧵 Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges https://lnkd.in/euaif-3G Nine quick tips for pathway enrichment analysis https://lnkd.in/e3sDvKfj https://lnkd.in/e5-MTcts Multiple sources of bias confound functional enrichment analysis of global -omics data Identifying significantly impacted pathways: a comprehensive review and assessment https://lnkd.in/ef9iQbxt Toward a gold standard for benchmarking gene set enrichment analysis https://lnkd.in/eAjYyHca Recurrent functional misinterpretation of RNA-seq data caused by sample-specific gene length bias https://lnkd.in/efwKqTa4 read this important thread on choosing background genes https://lnkd.in/e97MHbAS one of my old blog posts on GSEA https://lnkd.in/emkWscTR

Ultima Genomics launching high-end DNA sequencers that can read genome for $100 Excited to be working with Ultima Genomics on the commercial roll-out of the UG100 later this year! "The sequencer, dubbed the UG 100, is a $1.5 million machine that can read up to 20,000 human genomes a year. The reagents required to operate the instrument cost as little as $1 per billion sequenced DNA bases; that translates to $100 per genome" https://lnkd.in/eGfMKff6 #FOGBoston2024 #humangenome #nextgenerationsequencing

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The era of the $100 genome and beyond is here! Learn more about the the UG 100™ platform and how our early access customers have harnessed the power of genomics at scale.

Good better best( Gideon A. Wiafe ) ; ✨️ I keep saying environment matters; you'll be seen as useless in an environment without the resources to boost your skill or interest. You'll do well my dear fellow bioinformatician (Gideon A. Wiafe ) #Genomics #Bioinformatics #AMR #Cancer #Neuroscience