Questions tagged [metagenome]

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12 votes
5 answers
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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 ...
Konrad Rudolph's user avatar
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. ...
acvill's user avatar
  • 613
10 votes
3 answers
705 views

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 ...
deepseas's user avatar
  • 163
9 votes
2 answers
11k views

How to use Python to count k-mers?

I have some FASTQ sequence files and a FASTA file for some regions I'm interested in. I would like: Build an index for the FASTA file Use the index to count number of k-mers occurred in my sequence ...
SmallChess's user avatar
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6 votes
1 answer
110 views

What's the scaling for HOMER metagenes?

I'm trying to use HOMER to make a metagene profile over gene bodies using a bedgraph file I've generated. The problem is that every time I do, I get really weird scaling on the y-axis. I should be ...
bioinform_noob's user avatar
6 votes
1 answer
132 views

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 ...
Laura's user avatar
  • 909
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. ...
L R Joshi's user avatar
  • 719
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 ...
elsoja's user avatar
  • 241
5 votes
1 answer
217 views

Rapid metagenomics classifiers on long read data [closed]

I recently used the minION (Nanopore, 9.4 flow cell, RAD001 kit) to generate a metagenome out of environmental samples. Passed reads weren't brilliant (196, average 1,594bp lenght), but working with ...
André Soares's user avatar
4 votes
2 answers
622 views

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 ...
andresito's user avatar
  • 385
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 ...
h3ab74's user avatar
  • 836
4 votes
1 answer
181 views

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 ...
cbake's user avatar
  • 41
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 ...
Reebola95's user avatar
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 ...
schmiggle's user avatar
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. ...
Someone_1313's user avatar
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 ...
MagíBC's user avatar
  • 41
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 ...
M__'s user avatar
  • 12.1k
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 ...
Laura's user avatar
  • 909
3 votes
1 answer
73 views

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... ...
ljs's user avatar
  • 265
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 ...
Laura's user avatar
  • 909
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 ...
719016's user avatar
  • 2,324
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 ...
donkey's user avatar
  • 163
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 ...
gringer's user avatar
  • 13.9k
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. ...
Laura's user avatar
  • 909
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 ...
dunc4n's user avatar
  • 35
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, ...
Laura's user avatar
  • 909
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 ...
Ernie Hsieh's user avatar
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 ...
jh_'s user avatar
  • 81
2 votes
1 answer
54 views

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 ...
Rene's user avatar
  • 21
2 votes
1 answer
77 views

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 ...
lars20070's user avatar
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 ...
Avamys's user avatar
  • 118
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 ...
schmiggle's user avatar
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 ...
Laura's user avatar
  • 909
2 votes
0 answers
141 views

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 ...
Ahmed Abdullah's user avatar
1 vote
3 answers
255 views

Accidental mapping of eukaryotic reads in a metagenomic dataset

This is a question from /u/wipeyourmit on reddit. The original post can be found here. If I have a metagenomic dataset that contains reads from both eukaryotes and prokaryotes and then I annotate ...
gringer's user avatar
  • 13.9k
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 (...
DEEP's user avatar
  • 103
1 vote
1 answer
77 views

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 ...
DEEP's user avatar
  • 103
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 ...
gringer's user avatar
  • 13.9k
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 ...
Laura's user avatar
  • 909
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 ...
InterestingPenguin80's user avatar
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 ...
Laura's user avatar
  • 909
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?
Ahmed Abdullah's user avatar
1 vote
1 answer
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 ...
Rainman's user avatar
  • 161
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 ...
InterestingQuestions61's user avatar
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 ...
M__'s user avatar
  • 12.1k
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 ...
Poccia's user avatar
  • 13
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 ...
Nok Imchen's user avatar
1 vote
1 answer
45 views

Metagenomics: Identifying most common sequences

I am working on a project and used the following command: ...
DumbledoreTheGrey's user avatar
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, ...
Lamma's user avatar
  • 165
1 vote
2 answers
154 views

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 ...
Cody Glickman's user avatar