Create an Alignment of H3N2 Strains With Minimal Gaps

### **Aim**
Generate a new Multiple Sequence Alignment (MSA) from H3N2 strains (2011-2012, 2017-2018) with no gaps, with aligner settings as close to default as possible.

### **Hypothesis**
Seeing gaps and specific codes in the MSA will bring changes in sequences to our attention.

### **Method**
Filter Settings for fludb
- Use H3N2 strains from humans.
- Use calendar years 2011 and 2012 for one alignment, and calendar years 2017 and 2018 for another.
- Use full sequence length.

Verification and Trimming for Alignment
- Remove sequences with large gaps. Sequences with large gaps and low nucleotide count compared to other sequences are usually fragments.
- Remove sequences with internal gaps.
- Remove sequences with aligner-generated codes that don't indicate a single base (i.e. not A,T,C, or G). See [IUPAC Codes](https://www.bioinformatics.org/sms/iupac.html).
- Check for start and stop codons. They should be there.

### **Deliverables**
- Produce an MSA.
- Produce a Jupyter notebook that performs alignment verification and trimming.

### **GitHub Workflow**
Please fork & clone this repo. Check out a branch for your work, then push and make a PR for us to merge your notes & code to this repo. For an outline of how DCL repos are organized, see[ dir-struct.md](https://github.com/deepcelllineage/overview/wiki/dir-struct) in the overview wiki. Remember to .gitignore large data files, e.g. *.fasta and use .keep files to make git track directories that only have ignored files in them.

### **?**
Please put questions related to this issue in this issue thread. If you want a quick response, post a link to your comment in this thread to Slack #deepcelllineage or DM [@deena](https://github.com/deena). To join Slack enter your email address [here](http://bit.ly/JoinSlackFastaiSFbay). For questions NOT specifically related to this issue, get in touch through any of the communication methods listed in [DCL's overview README](https://github.com/deepcelllineage/overview/blob/master/README.md).