Tag: Kraken2

How to detect specific genes in metagenomics data 1 Hello, I have some shotgun metagenomics data (long reads sequenced by ONT). I want to use those metagenomics data in order to detect the presence of a specific gene (Cyp51) or its mutated homologous. I am a little bit confused because…

Add a genome to a kraken library 0 Hi, if I understood well, a kraken library only contains human, bacterial and viruses taxonomy. I noticed that it was possible to add another genome, as follows: kraken-build –add-to-library chr1.fa –db $DBNAME So I downloaded a genome, and write the following line:…

kraken on nt library 0 Hi, I’d like to perform a kraken library on the nt library, since my fastq sequences are not human I build a kraken nt library, as follows: kraken2-build –download-taxonomy –db nt Then the followng step, was to “kraken” my fastq file: kraken2 –db nt –output…

image: Runtime of GPMeta versus existing solutions view more  Credit: BGI Genomics Metagenomic sequencing (mNGS) is a powerful diagnostic tool to detect causative pathogens in clinical microbiological testing. Rapid and accurate classification of metagenomic sequences is a critical procedure for pathogen identification in the dry-lab step of mNGS tests. However, this…

Several studies have indicated the importance of gut microbes in maintaining human health. These microbes are also associated with fundamental physiologic processes, such as aging, drug response, nutrition, and pathophysiologic states (e.g., cardiovascular, metabolic, oncologic, neurological, and autoimmune diseases). To better understand the causal effects between gut microbes and disease…

Hi, @aitor.blancomiguez ,Question: I am getting the following error when running StrainPhlAn 4. I had some problems in step 5 “build the multiple sequence alignment and the phylogenetic tree”,Where could be a problem? What I should search for? Database： I’m using sample data(cmprod1.cibio.unitn.it/biobakery4/github_strainphlan4/) Command: strainphlan -s consensus_markers/*.pkl -m db_markers/t__SGB1877.fna -r…

false positives in taxonomic classification reports 0 Hello, For experts in metagenomics, I am using Kraken2 to do the taxonomic assignments. When testing it on simulated datasets or actual sequenced raw data, I see a lot of species and genera identified but with a very small number of sequences (under…

Hello, I am trying to build a costumed database, including all reference genomes of fungi, bacteria, archaea, viruses, and Homo sapiens. I am facing a problem in the first step: Creating sequence ID to taxonomy ID map. I had a message saying: Found 10361157/19252012 targets, searched through 948300298 accession IDs…..

. 2023 Mar 22;18(3):e0282428. doi: 10.1371/journal.pone.0282428. eCollection 2023. Sarah K Highlander  1 , Jason M Wood  2 , John D Gillece  1   3 , Megan Folkerts  1 , Viacheslav Fofanov  3   4 , Tara Furstenau  3 , Nitin K Singh  2 , Lisa Guan  2 , Arman Seuylemezian  2 , James N Benardini  2 , David M Engelthaler …

implementation of k-mer counting from krakenuniq to kraken2 1 Unless I am reading this wrong, authors say that KrakenUniq is only compatible with Kraken 1 databases, not Kraken 2. You may be able to choose a classifier using the advice on that page. Login before adding your answer. Traffic: 2220…

The Colorado potato beetle (CPB) is one of the most serious insect pests due to its high ecological plasticity and ability to rapidly develop resistance to insecticides. The use of biological insecticides based on viruses is a promising approach to control insect pests, but the information on viruses which infect…

Kraken2-folder of files as input 0 Hello, I am working with Kraken2 on Linux, I am working with this typical command and it works well: kraken2 –use-names –db $db_name –threads 8 –report reportname.report $fastq_file But I want to put a folder of fastq files as input not only a sequence….

Relation of the number of contigs to the real DNA abundance before sequencing 0 Hello everyone! I have a problem with my work on contigs. I have searched the literature but have not found anything useful yet. First, total DNA was isolated from a soil sample, then mechanically fragmented (sonication)…

Bacterial isolate Adolfo Lutz Institute is a regional reference laboratory for Salmonella isolates from São Paulo, Brazil. Thus, all isolates received are submitted to classical serotyping, antimicrobial susceptibility testing, and molecular-typing by PFGE and next-generation sequencing. Isolate 288_18 was recovered from a blood sample from a patient with clinical symptoms…

Hello dear all. My question is for people experienced in metagenomic analysis of complex microbial communities such as in soil. Suppose I have several soil shotgun metagenomes and I need to classify all of it reaching maximum possible diversity stored in my data. As far as I know, current full-genome…

Different results in finding human sequences from metagenomes (bowtie2 and Kraken2) 0 I’d like to remove human reads from human gut metagenomes. Many studies conduct bowtie2 to human genome and retain only unmapped reads. I did so, but many reads that did not mapped to human genome were annotated as…

Building a Simulated Metagenomic Dataset – HackMD       Published Linked with GitHub — tags: ‘JPL: Genetic Inventory Project’ — # Building a Simulated Metagenomic Dataset Here we’ll create a simulated metagenomic datasets for controlled testing. This dataset was used to determine the Kraken 2 confidence score that best…

Introduction Severe pneumonia is one of the most common causes of infectious diseases among patients in the intensive care unit (ICU), and this can lead to various complications and high mortality.1–3 Timely and accurate pathogen diagnoses are crucial for appropriate antimicrobial therapy and improved clinical outcomes. However, the low detection…

Article Highlight | 15-Jun-2022 Researchers leverage viruses identified from worldwide environmental samples to expand knowledge of viral taxa and their role in tree microbiomes DOE/US Department of Energy image: Analysis of metatranscriptome samples with novel viral taxa in Populus. (Top) Graphical abstract of the pipeline. (Bottom) Percentage read classification with novel…

Get reference genome from Kraken2 taxID 0 I have a ~10Gb ONT metagenome from citrus psyllid that I am trying to extract bacterial contigs from to assemble. My current thought for a pipeline is broadly as follows: Tentative ID of each contig with Kraken2, then QC to only take assignments…

Details Posted: 03-May-22 Location: Chicago, Illinois Type: Full-time Salary: Open Categories: Research – Laboratory/Non-Laboratory Staff/Administrative Location: Hyde Park Campus Job Description: Provides technical expertise in the selection, validation, and implementation of the appropriate internal and external data analytic and bioinformatic solutions needed to analyze specimens, process and integrate data, and…

16S is a very conserved sequence, which is why it’s used for targeted phylogenetic analysis; it makes it easy to amplify and analyse. Unfortunately that conservation is an issue with minimap2, which is built around the idea that matching scattered subsequences within a sequence is good enough for identifying matches…

Introduction The study of the microbial environments has benefited from the sequencing revolution, where technology improvement decreased the DNA sequencing cost and increased the number of sequenced nucleic bases. For approximately 20 years (depending on how we define the term metagenomics), it has allowed the decryption of the microbial composition…

We implemented a metagenomic DNA sequencing methodology to unbiasedly detect microbial species in CSF samples from patients with CNS symptoms in which a pathogen or EBV had been detected (Additional 3: Table 1). Samples positively identified with pathogen-specific quantitative PCR (qPCR), 16S rRNA gene sequencing or bacterial/mycotic culture in CSF…

Custom Kraken2 db 0 Hi, I have created a custom kraken2 database but it produced an unmapped.txt file with a list of accession numbers. 1) How do I find the taxa that have been included in this created db? 2) Is there a way to overcome this issue? For example,…

Kraken2 0 I wanted to make a kraken database but i got this error while running the command.I am using Kraken2 $ kraken2-build –standard –threads 24 –db kraken2database/ Downloading nucleotide gb accession to taxon map… done.Downloading nucleotide wgs accession to taxon map… done.Downloaded accession to taxon map(s)Downloading taxonomy tree data……

bash script not a valid identifier 2 I am trying to run bash script, but it gives this error ( `$fastq’: not a valid identifier). #!/bin/bash database=”kraken2_database” fastq=”fastq_dir” for $fastq in $(ls *_R1.fastq.gz | sed ‘s/_R1.fastq.gz//’) do kraken2 –db $database –threads 8 –memory-mapping –use-names –confidence 0.1 –report taxonomy_reads/${fastq}_kraken2.tax –paired ${fastq}_R1.fastq.gz…

Hi, can someone please check if these following steps are correct? I am trying to add to my plants kraken2 db (“plant_original”) few taxa genomes that I have downloaded from the NCBI website (alnus_glutinosa_GCA_003254965.1.fna, carpinus_fangiana_GCA_006937295.1.fna etc..). for file in *.fna do kraken2-build –add-to-library $file –db PATH/kraken/plant_original done Masking low-complexity regions…

Kraken2 output visualisation with Krona Viruses not shown 0 Dear all, I am trying to visualize my kraken2 output with Krona and the results look very doubtful. I build a metagenomic pipeline with multiple filtering steps and I should have mainly viral sequences (a brief look into my kraken2 output…