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In GitLab by @nhoffman on Dec 21, 2019, 11:21
Thinking about how to submit jobs for production pipelines for which there are file hierarchy conventions for input and output data... I just submitted a…
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Hi lime-bean
I am a Masters student at the University of Johannesburg, South Africa.
My project entails using eDNA metabarcording as a tool to study estuarine meacroinvertebrates.
Therefore the …
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Hi microbiome team,
Over in dada2 land we are interested in linking our package with other excellent Bioconductor microbiome packages. The primary way we have done this so far is to integrate "stubs"…
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**Improvement Description**
Provide a warning to the user when `--p-pooling-method` and `--p-chimera-method` are misaligned. In particular, `--p-chimera-method pooled` should only be used when `--p-p…
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[seqtab_no_chimeras_filtlen.rds.txt](https://github.com/YuLab-SMU/MicrobiotaProcess/files/8629999/seqtab_no_chimeras_filtlen.rds.txt)
[taxa_gtdb.rds.txt](https://github.com/YuLab-SMU/MicrobiotaProces…
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dada2 v1.2 just publicly released... it seems documentation/NEWS/etc are still v1.18 centric. I'm feeling a little hesitant to jump in until the ancillary stuff is brought up to speed. Thoughts?
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Can somebody help me with biobakery_workflows for 16s data? Below my script and errors:
biobakery_workflows 16s --input input --output out --method dada2 --pair-identifier "_R1_" --local-jobs 2 -…
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This seems to work pretty well with PacBio and Loop full length 16S runs and the full-length trained data. On our local cluster using the QIIME2 output from the pipeline:
```
module load QIIME2/2…
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Hi! Sorry if this is a rather silly question but I've been reading and couldn't find an answer on this one. I've been using Kraken2-Bracken on metagenomes and it runs great. I wanted to test the pipel…