Genomics: analysis and algorithms - seminární práce

Eubacterial genome assembly and annotation

• Use the data from exercise 8.
• Check the quality of input sequences (fastqc) and report including statistics.
• Perform assembly using the OLC algorithm (newbler) and deBruin graphs (e.g. velvet, Soap2, Abbyss).
• Compare assemblies and choose the best one.
• Choose one longer scaffold or contig and predict genes on it (glimmer).
• Use BLAST and/or FASTA (automated) to find the name of each gene.
• Present the workflow and results (number, size and quality of libraries, assembly quality, N50, etc., number of genes, annotation and its success, what you learned about the organism from the analysis).
• Either publish the presentation on the website or bring it on a USB drive. Any format is good: document, power point presentation, web page. An explanation of your workflow and a discussion of the results will be part of the exam.

Data

The data contains three libraries: paired-end from Illumina and two mate-pair from 454. The Illumina dataset is preprocessed: during quality control, some reads were removed, and the second paired sequence appears as single-end. To reduce computational complexity, we combined paired-end pairs that were so close to each other that they overlapped (extendedFrags), turning them into single-end reads as well. The remaining reads stayed paired (notCombined). (See also exercise 8.)

files: (GAA2024/E8_data)

single end (second pair is not there), MiSeq:
	Bcc7419-MiSeq-A895A-PE_1_U.fastq
	Bcc7419-MiSeq-A895A-PE_2_U.fastq
single end (joined paired-end), MiSeq:
	Bcc7419-MiSeq-A895A-PE_12_JOIN_P.extendedFrags.fastq
paired-end (paired-end without overlap), 600bp, MiSeq:
	Bcc7419-MiSeq-A895A-PE_12_JOIN_P.notCombined_1.fastq
	Bcc7419-MiSeq-A895A-PE_12_JOIN_P.notCombined_2.fastq

mate pairs, 3kbp, 454:
	Bcc7419-454-HB0RHHA02-PE_3k-UNIQ.sff
	Bcc7419-454-HAV0LKU05-PE_3k-UNIQ.sff