And the cluster link

Good idea, but there's more documentation about conda, and a lot of people I work with use the command line less than 5 hours per month.

I personally think it's because each amino acid change gets its own number

It'd really shift my way of thinking if it didn't

I think you misunderstand. There is a lot of coverage for these samples. So much so that it is hard to see bubbles or other aberrations.

How is this method simpler than what I attempted?

All 33 million+ reads were mapped with bbmap (all non-mapped reads were excluded prior to trimming the primers)

So, in summary, if high coverage samples aren't getting assigned lineages, I recommend subsampling them or adjusting the `samtools mpileup` command.

I really solved my dilemma (after too many hours trouble shooting it) by adding the `-d 0` flag to `samtools mpileup`, which uses a lot of memory but produced adequate consensus fasta files.

/

Instead it turns out that `bbmap` was allowing for very large insert sizes, some of which spanned the majority of the genome. These, for whatever reason, were given priority for `samtools mpileup` (which gets piped into `ivar consensus`) /

The most irritating part is that each of these 18 would generate a consensus that could be used for determining lineage if I subsampled them. I was worried about contamination, but these had all had human reads removed. /

Just remember to deactivate your environment when finished.

Popular bioinformatic tools have conda recipes, so conda helps make installing bioinformatic tools less painful.

6. Install stuff

I recommend installing tools in their own environment.

Something like

`conda create -n seqkit seqkit`

will install seqkit in a new conda environment named seqkit.

This environment can be turned on or activated with

`conda activate seqkit` /

5. Add some extra channels to conda.

I recommend conda-forge and bioconda

Something like this
`conda config --add channels conda-forge`

or this
`conda config --add channels bioconda`

Channels are where different conda packages are stored. Adding channels helps conda find packages to install. /

There are some people who then recommend installing mamba (or similar) with something like `conda install mamba`, which I think is fine. These tools perform similar tasks to conda, but are often faster. I let "more advanced" users explore these options and tend to keep everything "conda". /

4. Activate conda

Something like source `~/miniconda3/bin/activate`, or just log out and log back in

Now you have conda! /

3. Use bash (or whatever shell is being used) to run the downloaded script

`bash Miniconda3-latest-Linux-x86_64.sh`

Set all prompts with relevant information, and, yes, you want a line in your ~/.bashrc file

/