7 votes

How do I efficiently perform a metagenome screen of “all” species?

As you point out, BLAST is not going to work well for reads from a typical RNASeq experiment. From an RNASeq dataset, you might be able to get away with just a ribosomal screen using Silva, because ...
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  • 11.7k
7 votes

How to use Python to count k-mers?

I wrote a command-line k-mer counter called kmer-counter that will output results in a form that your Python script can consume: https://github.com/alexpreynolds/...
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5 votes
Accepted

How to use Python to count k-mers?

If you want to count the number of unique k-mers that occur in your data set, you should use the unique-kmers.py script, which implements a HyperLogLog-based cardinality estimator. If the number of ...
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4 votes

How do I efficiently perform a metagenome screen of “all” species?

I think you're just looking for nr. It is absolutely not limited to prokaryotes, far from it. It is, according to the blurb on the NCBI's blast page: The ...
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  • 8,121
4 votes

What's the scaling for HOMER metagenes?

Figured it out! For anyone who finds this thread in the future and is wondering what is going on: HOMER, when using the -size given option, normalizes the y-axis to the number of basepairs in the ...
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4 votes

How do I efficiently perform a metagenome screen of “all” species?

One thing that hasn't been suggested so far would be phylogenetic placement. First option there would be placing against one larger tree roughly touching the domains you mentioned to get an overview. ...
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4 votes

How do I efficiently perform a metagenome screen of “all” species?

You might want to look into minihashes as a more efficient way of clustering and comparing your sequences to known species and samples. In the mash paper the authors show how it would be feasible to ...
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4 votes
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Software for taxonomic assignment?

You could take a look at kraken2 It should fit your purpose.
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  • 609
4 votes
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Extract sequence context of high-degree nodes in assembly graphs

I don't have a recommendation of specific tools, but we might be able to use the GFA file itself to get at this with just bash commands. For these examples I use the linked GFA here, which is a ...
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3 votes

NCBI SRA database sample: control vs test

You can download the information using this link: I did it in R: ...
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  • 1,628
3 votes
Accepted

Transform traditional blast output to `--outfmt 6`

Biopython has a parser for Blast's default text format (which I assume is the one you have). Just use the blast-text string to specify this format in ...
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3 votes

Transform traditional blast output to `--outfmt 6`

The blast_formatter command allows you to produce output in any of the formats supported by BLAST. However, it requires that you run ...
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3 votes

Accidental mapping of eukaryotic reads in a metagenomic dataset

You can use centrifuge with the NT library to profile the taxonomy, and then remove the reads from eukaryotes.
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3 votes

Accidental mapping of eukaryotic reads in a metagenomic dataset

If you know the eukaryotic contaminant present you could use bbsplit.sh from BBMap suite to split/bin reads first using a reference for that contaminant (into one ...
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  • 59
3 votes

Software for taxonomic assignment?

If you like blast, maybe you can try DIAMOND - the authors claim it's much faster than BLAST.
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  • 86
3 votes

Extract sequence context of high-degree nodes in assembly graphs

Edit: I've written a short blog post describing my use of nodeSeqs.sh to investigate the functions of sequences at the nodes of short-read assembly graphs for a set of human oral microbiome samples. ...
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  • 443
2 votes

Pooling data in metagenome assembly

With metagenomes, there's several strategies and no one-size-fits-all. You can spend a lot of time playing with the data to try to get the "best assembly." But it depends on what you're trying to ...
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2 votes
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Viral Metagenomics

The specifics will depend on the experimental setup and data, but a few general comments... 1) Metagenomic data is often large volume and high in microbial diversity but low and uneven in coverage; ...
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  • 3,462
2 votes
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Is there a way to assemble contigs starting from a specific sequence?

This is one of the primary use cases for which spacegraphcats (preprint and code) was designed. The "neighborhood queries" discussed in the paper sound particularly relevant. I don't have any personal ...
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2 votes
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Comparing gene abundances between metagenomes

I would avoid using assemblies to answer this question, as there's no guarantee that you will be able to assemble your genes of interest; you can however estimate their abundance even if they are ...
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2 votes

How identifiable are human omics data and how to mitigate their identifying features?

This is one of the major problems with genomic information in todays research. This was highlighted some years ago with the police using publicly available genomic data bases to idenitfy unkown murder ...
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  • 768
2 votes
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Reads count in metagenomics

I think that there is a good argument for using technologies adapted from RNA-seq for metagenomic abundance quantification. The tool that I am most familiar with (that I use for this purpose) is ...
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2 votes
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Demovir produces an empty output

maybe you can open the demovir.R file with Rstudio and execute line by line to check where the failure is. - @zorbax Thanks for your suggestion. I eventually got a correct final output already. The ...
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2 votes

Co-occurrence networks in Metagenomics studies

To answer your question more formally. I strongly believe you are treating the mice with something that will shift its microbial flora. Clearly the experiment is not described. Thus what I simply feel ...
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  • 7,319
2 votes

Minimap2 detects too many 16S sequences in metagenome

16S is a very conserved sequence, which is why it's used for targeted phylogenetic analysis; it makes it easy to amplify and analyse. Unfortunately that conservation is an issue with minimap2, which ...
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  • 11.7k
2 votes

Phylogenetic tree rooting in shotgun metagenomics

The answer really is that a root is determined using external evidence, rather than from the internal branches. An algorithm such as root digger can be used to estimate the root placement based on a ...
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  • 7,319
2 votes
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How can I improve or otherwise investigate an unreliable genome tree?

The difficulty in answering the question is: The absence of "Y" in the "Gene of interest" tree The sampling bias in the number of taxa mostly between the "genome tree" ...
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  • 7,319
2 votes
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How to make pan-core genome curve through command line on linux?

The command create_pan_genome_plots from Roary can create a plot like this:
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2 votes
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rRNA genes missing from metagenomic bins; is there a way to recruit them?

I considered mentioning this but considered it implausible. However, apparently people are actually able to use PE shotgun data to link rRNA genes to MAGs. This is something that is quite trivial with ...
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1 vote

Is there any value in scaffolding the output contigs of MEGAHIT assembler given a metagenomic dataset?

Update 2: It looks like your approach has actually been suggested here as one way to use the PE information. I guess megahit may not be really using the PE information anyways. I still believe that it'...
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