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The two error models currently built-in are based on fairly old genomics data. It'd be nice to base them on recent-ish metagenomes, or at least recent genomic datasets sequencing with most popular rea…
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Normalization how it is implemented now normalizes :
1. the single end/merged paired-end reads, but takes the unnormed paired end reads into account.
2. the paired end reads but takes the unnormed …
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"""
The authors conclude that the presence of multiple strains confounds assembly, and that it still challenges the latest sequencing technologies. They also conclude that “mock” communities are cruc…
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Hi Meren,
I'm running anvi-script-FASTA-to-contigs-db on a metagenome assembly that has about 180,000 contigs and keep running out of disk space on my work station. Is there a way to change the temp…
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"""
In Lines 34-80 the authors provide a very thorough explanation of previous assessment of assemblers, it does however not reach a clear conclusion nor provide direction as to why the study is warr…
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I encountered an error while running the assemble workflow on Atlas (version 1.0.19). From the counts_per_region_.log, the error was
`Warning: Unknown annotation format: gtf. GTF format is used.`
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ghost updated
6 years ago
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Hello,
I am getting the an 'exit code 1' error when trying to assemble some metagenomes, and the log appears to indicates
'assemble: unrecognized option '--bubble_level'
uknown option'
Below is …
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I use Python 3.6.2 for my main environment and created a new conda environment for Python 2.7.13 in which I installed MIDAS. I am trying to run MIDAS but I am encountering the following errors regard…
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Greetings, I am using Canu 1.6, on a grid (PBS). I am trying to assemble a metagenome. I am not entirely sure if this is a canu specific question, or a question that requires some insight into PBS jo…
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I would like to reduce my Illumina metagenome to something approaching unique sequences, i.e. remove sequences that are already represented (though not necessarily exact duplicates that could be remov…