Categories
Tag: Kraken2
Moderate Mapping percentage
Moderate Mapping percentage 1 Hi all, I received my sequenced transcriptome and genomic data from my service provider and started working with it. Both the DNA and RNA data passed quality metrics post trimming. But the mapping percentage comes out to be 90% using bowtie-DNA and 85% using Hisat2-RNA. I…
Metagenomic analysis of Mesolithic chewed pitch reveals poor oral health among stone age individuals
The specific environmental/history/collection context The Huseby Klev materials were unearthed and collected by archaeologists (including two of the co-authors of this article) during the excavation of this coastal hunter-fisher-gatherer site in the 90s50. The material assemblage was rich and well preserved: human bones, animal bones, plant remains and pieces of…
Senior Bioinformatics Scientist in Chicago, IL for University of Chicago (UC)
Details Posted: 19-Dec-23 Location: Chicago, Illinois Type: Full-time Salary: Open Categories: Research – Laboratory/Non-Laboratory Staff/Administrative Location: Chicago, IL Job Description: Development of an integrated data warehouse for symbiote including clinical, microbiome sequence, and metabolomic data. Management of DFI Biobank, MMF, and HMMF data within the Symbiote platform. Functional analysis of…
Senior Bioinformatics Scientist @ University of Chicago
Department BSD DFI – Translational Informatics About the Department The Duchossois Family Institute focuses on the role of commensal bacteria in enhancing disease resistance and is using genomic and metabolomic platforms to characterize the microbiome and its metabolites. Computational and bioinformatic expertise is required to understand how commensal bacteria impact…
Bioactive glycans in a microbiome-directed food for children with malnutrition
Collection and handling of biospecimens obtained from participants in the randomized controlled clinical study of the efficacy of MDCF-2 The human study entitled ‘Community-based clinical trial with microbiota-directed complementary foods (MDCFs) made of locally available food ingredients for the management of children with primary moderate acute malnutrition (MAM)’ was approved…
Microbial gene coverage from blast result
Microbial gene coverage from blast result 0 Hello all I am new to BLAST and Biostars. I have removed human-mapped reads from RNA-Seq data and did Kraken2 and Bracken analysis using the microbial reads. Using the Kraken Tool, I retrieved the microbial reads. Then I performed BLASTx in order to…
Metagenome profiling and containment estimation through abundance-corrected k-mer sketching with sylph
Profiling metagenomes against databases allows for the detection and quantification of microbes, even at low abundances where assembly is not possible. We introduce sylph, a metagenome profiler that estimates metagenome-genome average nucleotide identity (ANI) through zero-inflated Poisson k-mer statistics, enabling ANI-based taxa detection. Sylph is the most accurate method on…
A streamlined pipeline based on HmmUFOtu for microbial community profiling using 16S rRNA amplicon sequencing
Microbial community profiling using 16S rRNA amplicon sequencing allows for taxonomic characterization of diverse microorganisms. While amplicon sequence variant (ASV) methods are increasingly favored for their fine-grained resolution of sequence variants, they often discard substantial portions of sequencing reads during quality control, particularly in datasets with large number samples. We…
`No preliminary seqid/taxid mapping files found, aborting.`
kraken2 database error: `No preliminary seqid/taxid mapping files found, aborting.` 0 Hi all, I’m putting this here in hopes that someone will understand and solve this issue for future users. This is already a known and apparently unsolved issue per this thread: github.com/DerrickWood/kraken2/issues/291 I am simply documenting this in hopes…
kraken2 database does not contain necessary file taxo.k2d
kraken2 database does not contain necessary file taxo.k2d 0 Hello everyone, I am trying to install use Kraken2 locally and am getting the error: kraken2: database (“./mydb”) does not contain necessary file taxo.k2d The database was built with the standard command: kraken2-build –standard –db mydb I don’t understand why this…
RVFScan predicts virulence factor genes and hypervirulence of the clinical metagenome | Briefings in Bioinformatics
Abstract Bacterial infections often involve virulence factors that play a crucial role in the pathogenicity of bacteria. Accurate detection of virulence factor genes (VFGs) is essential for precise treatment and prognostic management of hypervirulent bacterial infections. However, there is a lack of rapid and accurate methods for VFG identification from…
kraken2 bacteria database 250GB+
kraken2 bacteria database 250GB+ 0 Hi all, I’ve been trying to get Kraken2 installed locally and the main database is clearly far too large. I got 16S greengenes working fine and so now I’d like to try a larger database, the entire bacterial database. I don’t understand why it is…
How to proceed after Kraken2 analysis
How to proceed after Kraken2 analysis 0 Hello, I am working on tracking and tracing of viruses in plant seed lots. I have total RNAseq data from the seed lots (around 200 samples). I did a kraken2 analysis to fish out certain viruses which we are interested in. For each…
very few sequences classified with Kraken2
very few sequences classified with Kraken2 0 Hello all, I am trying to do taxonomy analysis via the 16S region of the bacterial genome from whole genome shotgun metagenomics samples. I installed Kraken2 and a 16S library called greengenes. After running kraken2 with this library and my aligned fastq files…
mv Question during kraken2-build (building database)
mv Question during kraken2-build (building database) 1 Hello all, I’d downloaded and installed Karken2 locally on WSL Ubuntu. After install, I build a standard database with the command: kraken2-build –standard –db databasename here is the out: Downloading nucleotide gb accession to taxon map… done. Downloading nucleotide wgs accession to taxon…
error importing Bracken database – Community Plugin Support
Has anyone had any luck importing a braken database? Managed to get kraken2 to work by downloading a one of the tar.gz files, extracting and only keeping the ‘k2d’ files and running: qiime tools import \ –type ‘Kraken2DB’ \ –input-path k2_pluspfp_16gb_20231009_q2 \ –output-path k2_pluspf.qza But trying something similar with –type…
Low Fraction Gene Expression Reads in Spots in Visium 10x Fresh Frozen experiment
Hello, I would like some expert advices about a problem that I encountered. I’ve been analyzing some samples from Visium 10x FF, and I aligned my fastqs with spaceranger. First, I aligned my histological images manually with Loupe, and I provided the .json file to spaceranger. What happened is that…
Metagenome sequencing and recovery of 444 metagenome-assembled genomes from the biofloc aquaculture system
Uncultured microorganisms constitute a significant proportion of microbial populations in an ecosystem and play a vital role in its functioning1. The challenges associated with cultivating these microbes have constrained access to the vast phylogenetic and functional diversity they possess. However, recent advancements in metagenomics have opened a new window to…
Distribution tendencies of pathogens causing LRTI
Introduction Lower respiratory tract infection (LRTI) remains one of the leading causes of death worldwide.1 Several well-known pathogens, including Streptococcus pneumoniae, Pseudomonas aeruginosa, Klebsiella pneumoniae, Candida, Herpesvirus, and others, have been identified as significant causes of infection.2 Nonetheless, nearly half of the cases still have an undetermined etiology,3,4 despite the…
Kraken2 is falsely assigning Klebsiella
Kraken2 is falsely assigning Klebsiella 1 Hi everyone! I’ve been running Kraken on a couple of clinical related samples (metagenomes) using Kraken2/Bracken using the silva Database. As a sanity check I run the same workflow on a mock community (SRR8073716) using different confidence values (0.1, 0.3 and 0.5). The classification…
The Clinical Impact of mNGS for the Diagnosis of PJI
Introduction The total number of periprosthetic joint infection cases is increasing with the surging numbers of joint arthroplasties, internal fixation implantation and the use of immunosuppressive agents.1,2 Unfortunately, the identification of corresponding pathogens remains time-consuming and challenging because of inert bacteria, biofilm formation and prior antibiotic administration.3–8 Metagenomic next-generation sequencing…
Kraken2 recovering only classified reads
Kraken2 recovering only classified reads 1 Hi everyone! I’m running Kraken2 on different metagenomes (Illumina paired end). I’m currently using it this way: kraken2 –output Sample_1 –paired Sample_1_R1.fastq Sample_1_R2.fastq With this I get everything running ok and get a single file with both classified and unclassified sequences. I would like…
Pipeline validation for the identification of antimicrobial-resistant genes in carbapenem-resistant Klebsiella pneumoniae
In this study, we validated a bioinformatics pipeline for K. pneumoniae identification and the prediction of antimicrobial resistance genes in sequenced samples obtained from humans infected with this pathogen. The K. pneumoniae genome has approximately two thousand conserved genes11,21. It also presents an accessory genome consisting of genes located on…
NCBI nt seqid2taxid.map
NCBI nt seqid2taxid.map 0 Hi all, I was wondering if anyone could share with me a link to a seqid2taxid.map that would be built when generating a Kraken2 database for NCBI. I need it to make a taxonomy.csv file for use with KrakenTools. However I downloaded the database from here…
Syntrophic entanglements for propionate and acetate oxidation under thermophilic and high-ammonia conditions
Reactor performance revealed temporal changes in propionate degradation rate The four propionate- and acetate-fed reactors used in the study produced biogas with an average methane content of 62–70% (Table S2). The pH was 8.1–8.3, resulting in an ammonia-nitrogen level of 0.7–0.9 g NH3 L-1. This free ammonia level is well above…
High classification percentage on Kraken2?
High classification percentage on Kraken2? 0 Hi all, I am running Kraken2 on some water eDNA samples. I am getting unusually high classification – only around 35% of my reads are classed as ‘unclassified’. I know of other people who run similar analysis on water samples and their classification success…
metagenome – What alternatives are there to Bracken?
metagenome – What alternatives are there to Bracken? – Bioinformatics Stack Exchange …
Azure vs AWS for cloud computing with Kraken2?
Azure vs AWS for cloud computing with Kraken2? 1 Hi, I am looking to set up a system to store genomic data and run Kraken2 in the cloud (I have a 32GB RAM machine which I don’t think will be able to load my ~9TB genomic database). Does anyone have…
Comparative analysis of carbapenem-resistant K. pneumoniae
Introduction The worldwide spread of Klebsiella pneumoniae is a major global public health threat.1,2 K. pneumoniae is an opportunistic pathogen that colonizes the human gut and respiratory tract and possibly causes infection in immunocompromised hosts. Gut colonized K. pneumoniae is one of the important pathogens causing nosocomial infections, although the…
Kraken2 nucleotide custom database
Kraken2 nucleotide custom database 0 Hi, I am using Kraken2 for metagenomic binning of my shotgun eDNA data. I am using a custom database of only aquatic organisms – this currently contains genome assemblies, and I am hoping to add nucleotide sequences to this database too. Is it a good…
Extract the true single-cell RNA sequencing reads for running SAHMI
Hello everyone! I’m currently using the SAHMI pipeline to annotate microbiome information from the single-cell data. However, I encountered two potential problems when applying SAHMI to 10X scRNA data: The first one is that SAHMI (SAHMI)inputs both paired reads to annotate microbiome by using kraken2, which calculates k-mer of assigned…
Kraken2 + Bracken with short reads (~20 bases) as input
Kraken2 + Bracken with short reads (~20 bases) as input 0 I have small RNA sequencing data (fastQC read length graph below) from rat tissue across two conditions and would like to investigate the presence of microbiome-sourced RNA. I have added the read length graph from an example fastQC report….
FINDFUNGI Pipeline
Forum:FINDFUNGI Pipeline 0 Hello guys, did anyone work with findfungi pipeline for metagenomics data before? Am using it right now and it doesn’t seem to work since it uses kraken 0.10 beta and it’s not available anymore so i tried using kraken2 but no solution, is that why it’s not…
First metagenomic analysis of the Andean condor (Vultur gryphus) gut microbiome reveals microbial diversity and wide resistome [PeerJ]
Introduction Vultures are obligate scavengers, birds of prey that provide several ecological services such as nutrient recycling or avoiding soil contamination by carcass feeding, which help to reduce the spread of diseases in their habitats (Ogada, Keesing & Virani, 2012; Chung et al., 2015; Buechley & Şekercioğlu, 2016). Vultures are…
Blastn and Kraken2 short reads clssification
Hello everyone, I’m reaching out to those familiar with nucleic sequence classification software such as Blastn and Kraken2. After performing shotgun sequencing on DNA extracted from a soil sample, I attempted to classify the obtained reads using Kraken2 software. To do this, I created a database containing sequences of bacteria,…
Genomic screening of 16 UK native bat species through conservationist networks uncovers coronaviruses with zoonotic potential
Sample collection Sampling kits were sent out to various bat rehabilitators in the UK, as described previously56, for the collection of faeces from bats. These faecal samples (0.02–1 g) were immediately stored in 5 ml of RNAlater solution to prevent degradation of RNA. The geographical locations and collection dates for all samples…
OTU, ASV and Kraken2
OTU, ASV and Kraken2 0 Hello everyone, I’m seeking clarification on the relationship between OTU, ASV, and Kraken2, which confuses me. I understand that with the OTU approach, sequences are grouped into clusters if they have a similarity above a pre-set threshold, and these sequences are then compared to a…
The Biostar Herald for Thursday, June 15, 2023
The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan…
How to detect specific genes in metagenomics data
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
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
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…
Introducing GPMeta: Ultrarapid GPU-accelerate | EurekAlert!
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…
Revealing their global influence on health
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…
Processing samples… error during StrainPhlAn 4 run – StrainPhlAn
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
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…
unmapped sequences during the first step of building the database #708
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…..
Multi-faceted metagenomic analysis of spacecraft associated surfaces reveal planetary protection relevant microbial composition
. 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
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 Metagenomic Analysis of Viral Diversity in Colorado Potato Beetle Public NGS Data
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
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
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)…
Whole genome sequence analysis of the first reported isolate of Salmonella Agona carrying blaCTX-M-55 gene in Brazil
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…
Classifying shotgun metagenomes with 16S rRNA database.
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)
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
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…
Bronchoalveolar Lavage Fluid for Metagenomic Sequencing
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…
A new approach produces a 90-fold increase in
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
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…
Director of Bioinformatics in Chicago, IL for University of Chicago (UC)
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…
Minimap2 detects too many 16S sequences in metagenome
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…
Frontiers | Machine Learning and Deep Learning Applications in Metagenomic Taxonomy and Functional Annotation
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…
Optimization of cerebrospinal fluid microbial DNA metagenomic sequencing diagnostics
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
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
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
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…
Adding new taxa to a Kraken2 db
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
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…