Questions tagged [metagenome]

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31 views

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 ...
1 vote
0 answers
63 views

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 ...
2 votes
3 answers
36 views

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 ...
1 vote
1 answer
91 views

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 ...
1 vote
1 answer
133 views

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 ...
1 vote
1 answer
62 views

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 ...
-1 votes
1 answer
40 views

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 ...
2 votes
1 answer
46 views

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 ...
2 votes
2 answers
71 views

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. ...
0 votes
1 answer
113 views

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 ...
1 vote
0 answers
66 views

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(...
2 votes
2 answers
52 views

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 ...
4 votes
1 answer
92 views

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 ...
1 vote
3 answers
111 views

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 (...
0 votes
1 answer
170 views

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 ...
1 vote
1 answer
56 views

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 ...
1 vote
1 answer
513 views

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 ...
2 votes
1 answer
73 views

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 ...
1 vote
1 answer
83 views

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 ...
2 votes
0 answers
30 views

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 ...
1 vote
0 answers
31 views

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.
1 vote
1 answer
82 views

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 ...
2 votes
0 answers
101 views

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 ...
2 votes
1 answer
110 views

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 ...
2 votes
1 answer
35 views

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, ...
3 votes
1 answer
87 views

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. ...
3 votes
1 answer
56 views

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 ...
3 votes
2 answers
170 views

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 ...
10 votes
2 answers
257 views

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. ...
5 votes
2 answers
318 views

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 ...
0 votes
1 answer
101 views

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 ...
1 vote
3 answers
673 views

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?
3 votes
1 answer
62 views

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 ...
5 votes
1 answer
155 views

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. ...
2 votes
1 answer
58 views

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 ...
4 votes
0 answers
921 views

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 ...
2 votes
0 answers
105 views

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 ...
1 vote
0 answers
181 views

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 ...
1 vote
1 answer
950 views

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 ...
0 votes
2 answers
98 views

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 ...
1 vote
1 answer
148 views

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, ...
3 votes
2 answers
722 views

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 ...
1 vote
0 answers
46 views

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 ...
0 votes
1 answer
242 views

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 ...
1 vote
0 answers
49 views

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 ...
1 vote
0 answers
137 views

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 ...
1 vote
1 answer
45 views

Metagenomics: Identifying most common sequences

I am working on a project and used the following command: ...
2 votes
2 answers
65 views

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 ...
0 votes
2 answers
85 views

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, ...
1 vote
1 answer
184 views

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 ...