Original goal:

1. Download the reads from a fairly well finished genome → Human chr.21
2. and assemble it using two or more standard assemblers → e.g. Celera Assembler, Mira
3. Compare the results using layout software (→ OSLay) and genome comparison programs

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Assembling:

• Downloaded reads (fastq) and alignments (BAM) from 1000 Genomes project
• Converted BAM to SAM and selected readnames, which mapped on Chr. 21
• Created new fastqs containing only selected reads

• Installed assembler wgs and mira
• Created frg-files from fastq-files (necessary for wgs)
• Problems running wgs

Plan B:

• Simulated contigs from Chr. 21
• Cut sequence
• Change order and orientation of contigs

Calculating local alignments between contigs:

• Megablast
• Problems:
  • Fasta identifiers are not allowed to be changed !!!

OSLay:

• Input of chr. 21 (~ 34 MB) is too large for OSLay

Plan B:

• Used segment of chr. 21 (~210 KB)

1st round:

• Assembly A: Sequence divided by 100
• Assembly B: Sequence divided by 19
• Run OSLay and adjusted parameters (→ assemblies are from the same sequence)
• Results: there are still 4 / 5 supercontigs → too many similar contig borders in simulated assemblies

2nd round:

• Created contigs with random length
• Assembly A: contigs of length 500 - 5000 bp
• Assembly B: contigs of length 1 - 200 KB
• Run OSLay and adjusted parameters
• Same parameters as in the 1st round → better results
• Results: 3 / 3 supercontigs (1 huge, 2 small)