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Generate test datasets for both short read and long read functionalities, host in a different github repo in the Arcadia-Science repo so it doesn't bloat the workflow repo. Full-size datasets for full…
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Dear Josh,
Hope all is well. Erfan here again. I wanted to also kindly request for there to be tutorials for people hoping to insert themselves at a specific point of the pipeline.
Since the p…
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Potentially change repo and workflow name to just `metagenomics-nf` as when you run with `nextflow run Arcadia-Science/arcadia-metagenomic-assembly-nf ....` the Arcadia part is redundant in the repo/w…
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Recently, I'm working on viral metagenomics. I identified viral contigs using virsorter2 and then performed binning using vRhyme. Finally I obtained some viral MAGs (vMAGs). CheckV seems could only as…
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Dear Metabolic Team,
I recently installed your pipeline and used it to map metatranscriptomic sequences against metagenome assembled genomes (that I also have already annotated and with a inferred …
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In addition to MAG recovery, I am also interested in estimating the abundance/coverage of each genome (similar to what is done [e.g.] via CoverM). Your paper reads: "long reads were mapped to the abov…
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Hello,
I previously raised an issue about the test run and we fixed that in issue #38. However, with my real data I have run into new issues. This time, with four samples I am able to go through th…
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```
(aviary-dev3)cl5n007:20220715:~/git/aviary$ aviary --help
......:::::: AVIARY ::::::......
A comprehensive metagenomics bioinformatics pipeline
Metagenom…
wwood updated
2 years ago
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**Submitting author:** @ParkvilleData (Babak Shaban)
**Repository:** https://github.com/ParkvilleData/MetaGenePipe/
**Branch with paper.md** (empty if default branch):
**Version:** 1.1.5
**Editor:** …
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Hello,
I have an issue where SM does not run the binning algorithms because it does not find the config file. I am sure it is something simple I am missing, thank you in advance for taking a look.
…