| ... | ... | @@ -150,7 +150,7 @@ rm coverage_of_references.done |
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## Chapter IV - Metagenome-assembled genomes (MAGs)
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- When you're having so much fun, why give up so soon?!
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- We had assemblies, gene calls, coverages, and comparisons between gene calls
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- So, we decided to go the full monty, a.k.a., "can we bin MAGs and will there be differences (if any)?
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- So, we decided to go the full monty, a.k.a., "can we bin MAGs and will there be differences (if any)?"
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- Note: the differences were expected, but we are scientists - we need data to validate!!
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```
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###################
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| ... | ... | @@ -480,7 +480,7 @@ done >> cluster_plots |
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```
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## Chapter XI - The miscellaneous or nearly-forgotten side projects
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- Due to the multifaceted nature of the best, i.e. the modular workflow, we tested several aspects separately
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- Due to the multifaceted nature of the beast, i.e. the modular workflow, we tested several aspects separately
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- For example: since we used two mappers bwa-mem and minimap for the reads, we binned each sample separtely based on the mapper
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- Additionally, we needed to merge bam files for the "hybrid"-binning, so we compared bins using [sourmash](https://github.com/dib-lab/sourmash) and compared assemblies using [quast](https://github.com/ablab/quast)
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| ... | ... | |
