All Questions
Tagged with assembly metagenome
12
questions
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
103
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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 ...
- 13
2
votes
2
answers
79
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.
...
- 1,007
10
votes
2
answers
281
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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. ...
- 613
0
votes
2
answers
107
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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 ...
- 1,007
1
vote
1
answer
98
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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 ...
- 111
1
vote
1
answer
197
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 ...
- 1,007
3
votes
2
answers
788
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 ...
- 1,007
0
votes
1
answer
245
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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 ...
- 1,007
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 ...
- 1,007
5
votes
1
answer
158
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.
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- 719
10
votes
3
answers
723
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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 ...
- 163