Please discuss the paper provided in more detail and include at least one other paper on the topic in your presentation. Your presentation should take at least 15 and no longer than 20 minutes.
- General information regarding SARS-CoV-2
- Genome information
- Gene important for infection
- General overview of Covid discovery and surveillance
https://academic.oup.com/bib/article/22/2/631/6067880
Include information about your topic from at least one other peer reviewed paper in your presentation.
- Briefly explain NGS
- Briefly explain Illumina sequencing (Sequencing by synthesis)
- Paired-end vs single-end reads
https://pubmed.ncbi.nlm.nih.gov/30478097/
Include information about your topic from at least one other peer reviewed paper in your presentation.
- Explain Phred score
- Explain FASTQ format
- Importance
- Mention typical problems that occur
- good vs bad data
https://doi.org/10.1093/bioinformatics/btw354
Include information about your topic from at least one other peer reviewed paper in your presentation.
- Explain trimming & filtering and their differences
- Coverage
- Read length vs read quality
https://doi.org/10.1093/bioinformatics/bty560
Include information about your topic from at least one other peer reviewed paper in your presentation.
- Explain alignment
- Explain the underlying algorithms
- local vs global
- pairwise vs multi-sequence
https://pubmed.ncbi.nlm.nih.gov/2231712/
Include information about your topic from at least one other peer reviewed paper in your presentation.
- Explain the implementation
- Compare tools
- Use cases
https://doi.org/10.1093/bioinformatics/btp324
Include information about your topic from at least one other peer reviewed paper in your presentation.
- Explain different approaches (de-novo, reference-guided; short read, long read, hybrid)
- Explain the problem with repetitive sequence segments (repeats)
- Explain contigs
- Goals
https://www.nature.com/articles/nmeth.1935
Include information about your topic from at least one other peer reviewed paper in your presentation.
- Explain superior tool
- Compare different approaches
https://academic.oup.com/bib/article/22/5/bbab102/6210065
Include information about your topic from at least one other peer reviewed paper in your presentation.
- Importance
- Reference-guided vs reference-free
- Compare different approaches
https://doi.org/10.1186/s13059-019-1829-6
Include information about your topic from at least one other peer reviewed paper in your presentation.
- Decision heuristic for best assembly
- reference-guided vs reference-free
- Completeness
https://doi.org/10.1093/bioinformatics/btt086
Include information about your topic from at least one other peer reviewed paper in your presentation.
- Genomic variants (SNPs, SNVs, indels)
- Special features
- Compare to other tools
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-01993-6
Include information about your topic from at least one other peer reviewed paper in your presentation.
- Explain variant
- Explain different types of variants (VOC, VOI, VUM)
- GISAID
- Pango nomenclature
https://doi.org/10.1093/ve/veab064
Include information about your topic from at least one other peer reviewed paper in your presentation.