Questions tagged [metagenome]

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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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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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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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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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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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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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Why does the abundance of certain metagenome functions change when filtering by higher levels in MG-RAST (seed subsystems)

I am working with annotating my metagenomes through the MG-RAST pipeline, annotating them with taxonomy and function. For this study we are interested in understanding phosphorus metabolism. To ...
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Cross-checking metagenomics analysis via reference genomes

I'm looking at verifying metagenomic pipeline output for small genomes (viruses) on short read data. Background Most of the work in small-genome metagenomics is performed using bacteria and I'm ...
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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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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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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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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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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 ...
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Mapping contigs back to samples from co-assembled metagenome

In an attempt to increase the quality of our metagenomic assembly and ensure we capture low abundance species we are co assembling ~20 samples. However after the assembly we need to perform some ...
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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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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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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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Reads count in metagenomics

Background: I am developing a pipeline for metagenomic studies of human gut microbiote. In particular, I am mapping the reads data originating from shotgun whole genome sequencing onto a gene ...
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Analyzing and visualizing metagenomic data

I am starting out in metagenomics, Aim I wish to understand the whole analysis from the raw reads to interpretation. Background My current pipeline is used for: analyzing human gut microbiota cleans ...
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1 answer
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Metagenomics: Identifying most common sequences

I am working on a project and used the following command: ...
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2 votes
2 answers
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Software for taxonomic assignment?

I have a couple of hundred bacterial sequences of 2-30 genes of interest each, recovered from metagenomics. None of them encode rRNA. Normally I'd just BLAST the one gene I already know to be reliable ...
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How identifiable are human omics data and how to mitigate their identifying features?

Say a database were to store human omics datasets. The human subjects are known and the sample size is rather small in size initially (n=500). The database contains genomics, transcriptomics, ...
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4 votes
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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 ...
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Comparing gene abundances between metagenomes

My workflow until now: Find fragments of a marker gene in unassembled metagenomes > download and assemble metagenomes > recover the gene neighborhood / gene set of interest Right now I have a ...
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Is it conflicting: significant difference according to Wald test but not in PERMANOVA and ANOSIM to compare species abundances of metagenomic samples?

If there is no significant difference between two groups of metagenomic samples according to "Multivariate differential abundance tests" for example PERMANOVA and ANOSIM, does it makes sense to use "...
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Alternatives to phrap for merging contigs with overlapping ends?

I have bins from metagenomes generated with metabat2 on bitbucket/berkleylab/scr which are predicted as viral by MARVEL. MARVEL ...
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3 votes
2 answers
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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 ...
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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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NCBI SRA database sample: control vs test

I was trying to download some data from NCBI SRA (SRA059451). There are 27 samples available for SRA059451. But i am unable to understand which samples are 'control' and 'test' samples. Please help me ...
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Can I get longer contigs by changing MEGAHIT settings?

My current settings are megahit -r input.fq --num-cpu-threads 32 --min-contig-len 300 --presets meta-large -o output. I picked the 'presets meta-large' because I am ...
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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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2 votes
1 answer
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Metagenomic shotgun data with internal control

For 24 human stool samples I have metagenomic shotgun reads from an Illumina platform. The reads were filtered and mapped against a bacterial species library and specific maps to species were kept and ...
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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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How to apply RDP, Greengenes and other special taxonomies in Krona?

I used Kraken 2 to classify my 16S metagenomic data using both RDP and Greengenes database. As these are special databases the taxonomic ids assigned do not match with the NCBI taxonomic ids. I found ...
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6 votes
1 answer
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Is there a way to assemble contigs starting from a specific sequence?

My work involves searching for marker genes/fragments in metagenomic databases (like the Sequence Read Archive). Once I find these sequences, I would like to know more about the neighboring genomic ...
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2 votes
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API/website for blasting peptide sequence against database of all plant proteomes

I would like to blast a peptide sequence against all available plant proteome databases, i.e. a blastp metaproteome analysis. What tools are available? Which ...
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3 votes
1 answer
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How to query the Human Microbiome Project (HMP) to find all subjects with both 16s and WGS workups?

I am looking for a query to run on the HMP database that will return all subjects who have had BOTH 16s and whole genomes sequence (WGS) workups. I am currently using this query... ...
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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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What are Approximate Read Counts (Library Sizes) and Lengths (Insert Sizes) for Next-Generation DNA Sequencers?

I am performing a simulation study and am curious about the parameters of my simulated metagenome. What are the library and insert sizes of some of the most "used" sequencers. Mainly, I am ...
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4 votes
1 answer
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Using large databases with BLAT

I'm a computer scientist working with biologists at a small school that doesn't have dedicated bioinformatics staff. I apologize if I use incorrect terminology since I have limited bioinformatics ...
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4 votes
2 answers
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Transform traditional blast output to `--outfmt 6`

I have run a blastx of metagenomic databases (raw illumina reads) using the nr database. Unfortunately, I forgot to add the --outfmt 6 argument to the code and got ...
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5 votes
2 answers
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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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12 votes
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How do I efficiently perform a metagenome screen of “all” species?

I’ve got an RNA-seq dataset with a large proportion of environmental RNA “contamination”. BLASTing random reads reveals that much of the data comes from bacterial, plant and viral RNA. My target ...
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1 vote
2 answers
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Workflow of metabarcoding analysis

For a diet analysis of an insect-eating animal, all species in a sample shall be identified. For this a sequencing of the metagenomic sample was done, where the COI/COX region was used as a barcode ...
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10 votes
3 answers
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Pooling data in metagenome assembly

I have 12 human gut microbiome WGS Nextseq reads (151 bp paired end). What will be an effective strategy to assemble a metagenome? Let us say I have already filtered the fastq for quality, adapter ...
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