Questions tagged [metagenome]
The metagenome tag has no usage guidance.
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16S merging sequences, removes ALL reads
I am currently analysing some 16S (V4 region) rRNA data, using the qiime2 command-line software. Everything is working fine for the most part, until we are to merge the forward and reverse sequences - ...
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Normalization and Comparison of AMR Gene Tables from Long-Read Metagenomics Data without Spike-In Controls
I am conducting antimicrobial resistance (AMR) surveillance in water samples using long-read metagenomics (Nanopore sequencing). After analyzing the data with KMA (a k-mer read alignment tool, Clausen ...
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Understanding the Impact of Parameter Adjustment in KMA Aligner for Gene Analysis
I am currently using the KMA aligner (k-mer alignment) from Clausen et al. (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2336-6) to analyze gene sequences (metagenomics) and ...
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Understanding the Relationship Between ConClave Score, Depth, and Template Length in KMA Aligner Results
I am currently analyzing my nanopore metagenomic sequencing data. After demultiplexing and trimming, I am using the KMA (k-mer alignment) aligner by Clausen et al. (https://bmcbioinformatics....
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How adding genomes to a kraken database can increase the number of minimizers associated with a leaf of the taxonomy?
I built a protozoa kraken 2 database ("db1"), from which I further built two other databases ("db2" and "db3") by adding extra genomes in the Leishmania sub-genus*.
When ...
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short Read/percentage threshold for bacterium presence in metagenome
I have ~100 paired end short read human gut metagenome samples that I classified using Kraken2. Now I want to know if a specific bacterium is in any of those samples. As far as I've searched people ...
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How to design a synthetic wastewater FASTQ file that could be flagged as "engineered"?
I am an apprentice-level python user who occasionally works in medical laboratories and mainly does business work. I am presented with the unenviable task of orchestrating a proficiency test of some ...
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MMSeqs taxonomy running for over a day
I've been trying to run mmseqs2 on a few metagenomic assemblies and despite my best efforts in reading the wiki and playing with parameters, the process is taking over a day.
In their paper they claim ...
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Bracken not working
I have some highly contaminated ancient DNA sequences. I have adapter removed and collapsed these and run them through Kraken2. The Kraken reports show multiple levels of taxa with good numbers of ...
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detecting DNA of possible infection on cell line
we've done Whole Genome Sequencing with Illumina on DNA extracted from cell lines, where some are suspected to have been infected by something (viral, bacterial, not sure).
I've tried running ...
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Is 16S sequencing cheaper than whole-genome sequencing for taxonomic assignment?
This is adapted from a question posted on reddit
In my work, I occasionally get asked about metagenomic sequencing, which (after further questioning) I discover means that the person wants to work out ...
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Kraken2 Standard Database failing to build (unexpected FTP path)
I am attempting to build just the standard Kraken2 Database by using the following command:
kraken2-build --standard --threads 24 --db $DBNAME
I am returned the ...
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Variation in 16S rRNA between assemblers - how do I know which is real?
I have a low-diversity metagenome (~11 bins > 80% completion). Out of the bins, 3 are of interest to me. None of the lower-completion bins that can be identified are from the group of interest. So ...
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Feature-selection microbiome data to build a model to predict cancer
I want to build a machine learning model to predict colorectal cancer based on 16S rRNA microbiome data (stool samples).
I have filtered the data using filtering approach by Duvallet(removing samples ...
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What alternatives are there to Bracken?
Bracken is the recommended post-processer of Kraken2 outputs and specifically is expected to improve relative abundance estimates. However, Bracken's Github has over 100 outstanding issues and the ...
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How can I improve or otherwise investigate an unreliable genome tree?
Summary My genome tree doesn't agree with my gene trees and I get the feeling that my genome tree might be wrong, possibly due to long branch attraction, but I don't know how to check/fix it.
...
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How do I build the MinusB database for Kraken2? (Taxonomy issues)
I am attempting to build my own custom database for Kraken2. I have two questions:
If I have the MCPyV genome in a file called MCPyV.fasta, how do I build a database with just this?
How do I build ...
CommunityBot
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Can files with different R1 and R2 lengths be trusted?
I received paired end amplicon sequence from a LAB with different lengths for R1 (320) and R2(280). Should I trust this lab to sequence other samples?
Also, I had to do a trimming over the R2 at 220(...
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What would be the best method to obtain every prokaryotic psychrophile genome?
I am interested in running an analysis on the genome of every psychrophilic bacteria. Here defined as bacteria that have an optimal growth temperature at less than 15°C.
What would be the best way to ...
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Co-occurrence networks in Metagenomics studies
I have recently acquired some 16S metagenomics data, and was wondering if anyone can speak of the potential limitations, challenges as well as advantages to conducting a network-based study on ...
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Software for microbial profiling from 16S rRNA gene sequence
I have hundreds of GBs metagenomic 16S rRNA gene sequence data. I want to do microbiome composition profiling (with relative abundance) from the data. Also after that, I will do functional profiling (...
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Blast output file only shows 500 lines -outfmt 6
I had created databases of different sets of metagenome datasets - one with 6 runs, other with 48 runs, another with 100 runs, etc using the accession list for each of these datasets and makeblastdb ...
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eggNOG: DNA-DNA or protein-protein orthologue identification?
I'm trying to work out is how reliable/accurate my eggNOG metagenomic outputs are. Critical for this is how its identifying orthologues.
Background eggNOG is ...
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How do I build the "Standard Kraken 2 Database"?
I am at this point in the GitHub tutorial: https://github.com/DerrickWood/kraken2/blob/master/docs/MANUAL.markdown#standard-kraken-2-database
It says to create the standard Kraken database, I use the ...
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How do I measure the proportion of different bacteria in a sample from a high-throughput sequencer?
[this question is based on a question that was asked on Reddit]
I have sequenced some [mostly cell-free] DNA from a sputum sample on a nanopore sequencing machine, and would like to know what is in it ...
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How to quantifiy of specific genes from shotgun metagenome?
I have googled a "lot", couldn't find any specific answer to the question. So, I am here seeking for your guidance. My question is similar to this. I have several metagenome (n=30). But for ...
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MAGs transcriptomics pipeline question
I have currently a following problem. I have a one sample that I did my metagenomics on (Illumina shotgun + nanopore) and have recovered some high quality MAGs. I also did a metatranscriptomics on the ...
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Transcriptome analysis
I am trying to assemble reads belonging to two different readlength. Is it a valid way since I am looking for common genes among the species I am assembling.
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MetaQuast for assembling samples from complex communities
I'm working with whole genome metagenomic samples from human skin, and I'm using MEGAHIT for assembly and MetaQuast for evaluation. However, MetaQuast requires a list of reference genomes for the ...
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Krakenuniq mmap error
I built Krakenuniq on an HPC, and I've been trying to run it on my data using the following command:
krakenuniq --db DBDIR --threads 1 All_reads.fastq
This ...
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Generating contigs from illumina Paired End Reads (Metagenome)
I'm a wet-lab biologist desperately trying to get to grips with some Bioinformatics.
I have some shotgun Illumina paired-end data from a gut microbiome project I'm working on. I'm considering how to ...
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rRNA genes missing from metagenomic bins; is there a way to recruit them?
I have a couple of metagenomic bins which are okay in quality, but often missing rRNAs (16S, 23S...). I assume this is due to high population variability, combined with the high conservation of rRNAs, ...
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How to make pan-core genome curve through command line on linux?
I´m working with a dataset of 566 genomes to analyze a pangenome. So I was working with PANWEB to create this pan core genome curve, however, there is too much sequence to work with this webserver. ...
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Phylogenetic tree rooting in shotgun metagenomics
But I have some weeks fighting with this issue about phylogenetic tree building to use in a phyloseq object in order to calculate beta-diversity metrics that takes into account tree distance branches ...
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Minimap2 detects too many 16S sequences in metagenome
I'd like to extract bacterial sequences from a metagenome where ~99% of contigs are from a host insect. My current protocol minimaps every 16S sequences present in the sample, then blasts all those ...
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Extract sequence context of high-degree nodes in assembly graphs
I often use metaSPAdes to assemble short reads from human microbiomes. My simplified understanding of short-read de Bruijn graph assemblers is that they fail where ambiguous paths cannot be resolved. ...
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Microbial diversity analysis using whole-genome metagenomic data
I have data, obtained from a single metagenomic DNA sample, that consists of two MiSeq FASTQ files (R1 and R2) that I merged using PEAR.
Now I want to estimate the abundances of the bacteria taxa to ...
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Shotgun analysis: Where and how to start?
I am a complete rookie in shotgun analysis, having only performed marker gene analysis before. I have a pipeline that I want to try but I can't wrap my head around how it all works.
Please correct me ...
CommunityBot
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Python module for fetching NCBI id for a list of species
I have a list of scientific names of species. Is there a python module that can fetch NCBI taxonomy IDs?
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Metagenomics pipeline recommendations for short-read data
de novo metagenomics on viral NGS data is a hot-topic. On this site alone at least 4 specific algorithms have been used to identify multi-strain/multi-species for a given data set, however these do ...
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Viral Metagenomics
I am analyzing viral metagenomics data (Illumina Miseq) for the first time. I have used Ray (reference below) for de novo viral genome assembly before but I haven't done metagenomics analysis before.
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Demovir produces an empty output
I am new to bioinformatics and am working on viral metagenomic (virome) datasets and so would like to use Demovir* for doing taxonomic annotations on my viral contigs.
First, I installed all ...
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Kraken2 > OTU format > Phyloseq
A collaborator has passed me over Kraken2 outputs *.report and *.kraken, from a metatranscriptomic sequencing experiment conducted on the minION.
I would like to make a tree if the data using a ...
M__♦
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Does it make sense to compare the mean relative coverages for contigs / MAGs from samples that were not co-assembled?
I have a subset of high-quality MAGs from different environments, sequenced on different runs. I want to know, for any particular MAG, if it (or something similar to it) is present in any particular ...
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Removing adapters + primers from fastq files
I am currently in the process of removing adapters and primers from some 16S data acquired, and have a conceptual question regarding this pre-processing step:
So there are a series of different primer ...
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Searching for adapter sequences in FASTQ files - metgenomics
I have recently received some metagenomic data from 16S rrna sequencing. The sequencing company claim to have removed primers, however not adapter sequences. Please note that the files have been ...
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What are some ways to check metagenomic bin quality?
I am new to metagenomic binning. I've used CheckM in order to estimate completeness and contamination values, and most of my bins of interest appear to have good values. My workflow was pretty ...
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How to calculate coverage depth of genes in an annotated sequence?
I have a metagenomic dataset across multiple samples that has been grouped and binned (we did this due to poor sequence quallity).
It is several samples taken from termite guts of differing castes, ...
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Is there any value in scaffolding the output contigs of MEGAHIT assembler given a metagenomic dataset?
As far as I understood, for most assembly programs, the scaffolding step takes into consideration paired-end information in order to get from contigs (contiguous sequences) to scaffolds (longer ...
CommunityBot
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Which database is good to store (metagenomic) relative abundance data?
The simple question is: how to store relative abundance data in a database? Which database to choose?
I am talking here about metagenomics data, relative abundance of species or some features. Each ...
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