Questions tagged [metagenome]

The tag has no usage guidance.

Filter by
Sorted by
Tagged with
2
votes
0answers
27 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
0answers
34 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
1answer
40 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
2answers
32 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 ...
0
votes
1answer
53 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 ...
0
votes
0answers
7 views

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 ...
1
vote
1answer
22 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 ...
1
vote
0answers
31 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 ...
1
vote
0answers
40 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
1answer
66 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
0answers
35 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
1answer
30 views

Metagenomics: Identifying most common sequences

I am working on a project and used the following command: ...
2
votes
2answers
52 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
2answers
65 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, ...
2
votes
0answers
269 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 use this data in phyloseq, however, I ...
1
vote
1answer
61 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 ...
1
vote
1answer
47 views

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 "...
1
vote
0answers
48 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 ...
3
votes
2answers
317 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 ...
0
votes
2answers
41 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
1answer
58 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 ...
0
votes
1answer
106 views

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 ...
1
vote
1answer
76 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, ...
2
votes
1answer
40 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 ...
1
vote
3answers
191 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?
1
vote
0answers
93 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 ...
0
votes
0answers
26 views

Illumina 16S amplicon sequencing of healthy human cohort

I am looking for a 16S amplicon (ideally V3-V4) dataset from Illumina paired-end sequencing, which is similar to the healthy human cohort of the human microbiome project. I am primarily interested in ...
0
votes
0answers
26 views

How to build ML tree among OTUs and 16s sequence

I have OTUs sequence generated from 16s V4 clean reads, and want to build maximum likelhood tree with selcted taxonomy 16s refseq from Sliva database. ...
6
votes
1answer
94 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 ...
2
votes
1answer
69 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 ...
3
votes
1answer
69 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... ...
5
votes
1answer
134 views

Viral Metagenomics

I am analyzing viral metagenomics data (Illumina Miseq) for the first time. I have used Ray for de novo viral genome assembly before but I haven't done metagenomics analysis before. I know that there ...
1
vote
2answers
105 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 ...
4
votes
1answer
140 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 ...
4
votes
2answers
395 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 ...
3
votes
0answers
223 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 ...
12
votes
5answers
228 views

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 ...
1
vote
2answers
136 views

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 ...
9
votes
3answers
537 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 ...
8
votes
2answers
9k 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 ...
6
votes
1answer
70 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 ...
1
vote
3answers
239 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 ...
5
votes
1answer
207 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 ...