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I have obtained bins with a gene-based binning, these genes are generally short (
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The rnaSpades mode is heavily focused on mRNA transcriptome assembly and is very aggressive at splicing assemblies into short transcripts. The —meta mode would be more suitable for our DNA/RNA assembl…
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Could we add instructions in dahak for how users could extract specific sequences from metagenomes for further analysis?
@ctb recommended identifying the reference sequence of interest after using …
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Hi,
I get an error when trying to combine several OTU tables to one.
This command ran successfully:
for i in *.profile.tsv
do
name=$(basename $i profile.tsv)
singlem summarise --input-taxonom…
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**Paper**
- [CAMI II: identifying best practices and issues for metagenomics software](https://www.nature.com/articles/s41592-022-01419-0)
**Research Briefing**
- [Critical Assessment of Metageno…
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Thanks for the great tool! I am currently running tax_myPHAGE on a set of viral genomes reconstructed from metagenomic samples from the human gut. I was wondering if you have any recommendation when a…
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Hi,
I notice that while --similarity cutoff is by default mention as 0.95 it actually uses 0.80 cutoff while merging and clustering results from samples. I feel 0.80 is bit conservative. What do y…
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I got this error running in reference mode and I'm not sure how to diagnose.
```
rule run_centrifuge:
input: 03_CONTIGS/G01-gene-calls.fa
output: 03_CONTIGS/G01-centrifuge_hits.tsv, 03_C…
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I used the Bulk download script (https://github.com/ProteinsWebTeam/ebi-metagenomics/wiki/Downloading-results-programmatically) to download metagenomes per project (ProcessedReads fasta files) and it …