abeershalaby / nu-ngs01

NGS-1 Data analysis course

NGS Data analysis course-1

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Lectures

Day 1

1. Part 1 | Next generation sequencing Techniques [Canvas]
2. Part 2 | Data file formats for NGS "intro" [Canvas]
3. Part 3 | BASH [Lectures]

Day 2

1. Part 1 | Fastq exploration and seqkit_examples
2. Part 2 | FASTQC
3. Part 3 | Error trimming

Day 3

1. Part 1 | Sequence Alignment [Canvas]
2. Part 2 | Tutorial of Sequence Alignment
3. Part 3 | Git

Day 4

1. Part 1 | Algorithms for de novo assembly [Canvas]
2. Part 2 | Tutorial of de novo assembly
3. Part 3 | Reference based assembly [Canvas]
4. Part 4 | Tutorial of Reference based assembly

Day 5

1. Part 1 | Assembly Quality Assessment
2. Part 2 | functional annotation of Transcriptome assemply
3. Part 3 | Compare Transcriptome assemplies

Day 6

1. Part 1 | Differential expression
2. Part 2 | Assignment