Dear Developers and other users:
I'm now trying to use the mash screen to detect potential contaminants within my NGS data. Now I'm following a tutorial offered by the developers: https://mash.readthedocs.io/en/latest/tutorials.html#screening-a-read-set-for-containment-of-refseq-genomes.
I downloaded the pre-sketched RefSeq archive from the following website for my analysis: https://gembox.cbcb.umd.edu/mash/refseq.genomes.k21s1000.msh
When I manually inspect the results, I cannot find any reliable hits (identity >=0.95) in the outputs for some of my samples (the expected organism was not there also). I guess a possible reason is that the pre-sketched refseq database offered by the developer was too old and not only my expected organism but also the potential contaminant were not included.
My question: Can anyone tell me the release version of refseq database?
In a previous issue in 2020 #139, the RefSeq release version was release 93
A related question: Does anyone try to establish a sketched RefSeq database using the latest release manually? I'm looking forward to any suggestions on this idea!
Best,
Guo-Song
Dear Developers and other users:
I'm now trying to use the
mash screento detect potential contaminants within my NGS data. Now I'm following a tutorial offered by the developers: https://mash.readthedocs.io/en/latest/tutorials.html#screening-a-read-set-for-containment-of-refseq-genomes.I downloaded the pre-sketched RefSeq archive from the following website for my analysis: https://gembox.cbcb.umd.edu/mash/refseq.genomes.k21s1000.msh
When I manually inspect the results, I cannot find any reliable hits (identity >=0.95) in the outputs for some of my samples (the expected organism was not there also). I guess a possible reason is that the pre-sketched refseq database offered by the developer was too old and not only my expected organism but also the potential contaminant were not included.
My question: Can anyone tell me the release version of refseq database?
In a previous issue in 2020 #139, the RefSeq release version was release 93
A related question: Does anyone try to establish a sketched RefSeq database using the latest release manually? I'm looking forward to any suggestions on this idea!
Best,
Guo-Song