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Identify all (meta)genomic datasets that meet certain environmental measurement thresholds (e.g. all samples at X°C, with Y nitrate concentration, Z phosphate concentration)
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For plasmid you will not get a good result if you just use the default settings.
I would recommend getting GENBANK files (.gbk or .gb) of all the plasmids that are similar to your one.
Say you g…
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Hi sourmash team! Is there a way to identify which reads in a metagenome have/have not been classified after running 'sourmash gather' and 'sourmash tax'? For example, a list of read IDs might be gene…
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When I run `phylosift search -help` it went error with following:
> NCBI taxonomy data not found and unable to connect to update server, please check your phylosift configuration and internet conn…
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I just ran gather on some genomes (attaching a snippet of results below). These are all single genomes.
```
overlap p_query p_match avg_abund
--------- ------- ------- ---------
5.3 Mbp …
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Hell Dashing2 developer,
Dashing can be use for genome derelication in nt format but I am wondering wither it is an option to have it also work for amino acid sequences (all gene of a genome in ami…
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# Bug Report
### Affected tool(s) or class(es)
PathSeq
### Affected version(s)
- 4.1.6.0
### Description
I wanted to better understand the PathSeq pipeline (and in particular, the Host…
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Hello!!
I have converted the protein sequences into the OrthoMCL readable format using bioawk tool. My program is running but while at the stage 9 it shows me that the parseBlast.log command faile…
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# Title
Exploring and solving functional analysis gaps in metaproteomics.
# Abstract
Metaproteomics, the study of the full protein complement of microbial communities, is becoming an increasi…
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## Motivation
Pangenomes are key to understanding the distribution of gene content and synteny across closely related genomes. Currently, the driving force behind this strategy is sequence alignmen…