Questions tagged [metagenome]
The metagenome tag has no usage guidance.
71
questions
0
votes
0
answers
12
views
Understanding the Relationship Between ConClave Score, Depth, and Template Length in KMA Aligner Results
I am currently analyzing my nanopore metagenomic sequencing data. After demultiplexing and trimming, I am using the KMA (k-mer alignment) aligner by Clausen et al. (https://bmcbioinformatics....
- 31
3
votes
2
answers
68
views
short Read/percentage threshold for bacterium presence in metagenome
I have ~100 paired end short read human gut metagenome samples that I classified using Kraken2. Now I want to know if a specific bacterium is in any of those samples. As far as I've searched people ...
- 33
-1
votes
1
answer
42
views
How to design a synthetic wastewater FASTQ file that could be flagged as "engineered"?
I am an apprentice-level python user who occasionally works in medical laboratories and mainly does business work. I am presented with the unenviable task of orchestrating a proficiency test of some ...
1
vote
1
answer
63
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 ...
- 171
1
vote
1
answer
95
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 ...
- 14.7k
1
vote
1
answer
71
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 ...
- 1,007
-1
votes
1
answer
45
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 ...
- 37
2
votes
1
answer
72
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 ...
- 101
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 ...
- 2,344
1
vote
0
answers
88
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(...
- 11
1
vote
0
answers
101
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 ...
- 11
2
votes
2
answers
77
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 ...
- 163
0
votes
1
answer
248
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 ...
- 149
0
votes
1
answer
138
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 ...
2
votes
1
answer
224
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 ...