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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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Hi
I used contigs mode o bin the metagenomes (long-reads).
Then I am trying to run the separate_reads.py and I am getting the following error:
```
Traceback (most recent call last):
File "sepa…
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Hi CAMISIM,
Thanks for the great tool. I have just started to use it to generate metagenomes based on a custom profile. Since I am using genomes of assemblies of relatively new strains, I am using …
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[InStrain enables population genomic analysis from metagenomic data and rigorous detection of identical microbial strains](https://www.biorxiv.org/content/10.1101/2020.01.22.915579v1)
Coexisting mi…
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crunching numbers on contig-level stats in #73 I get --
strict:
ContigInfo.NO_IDENT 120035 contigs / 599.6 Mbp
ContigInfo.CLEAN 109778 contigs / 1193.3 Mbp
ContigInfo.NO_HASH 6079 contigs / 19.0…
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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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This would be used in cases where non-complex metagenomes do not require a high amount of sequencing coverage to capture all of the necessary information.
It would be an option for dahak users to i…
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I have obtained bins with a gene-based binning, these genes are generally short (