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Old 02-19-2014, 02:06 PM   #1
Location: Sydney

Join Date: Feb 2014
Posts: 20
Default Best way to perform assembly with two sets of raw data

Best way to merge data from two separate sequence runs

We have performed 2 sequencing runs of a bacterial organism with a genome about 4.4Mb. One was performed a few years ago by BGI and we again sequenced the same organism a few weeks ago. I am trying to determine the best way to go about the assembly.

1) Merge the 4 fastq files and perform the assembly as normal.

2) Map the reads of the second assembly to a fasta file of the first assembly.

3) Align the two individually assembled genomes.

4) Are there any other methods I haven't thought of.

Just a side note - from looking at the raw data - I think the first assembly has less contamination then the second run (these organisms are prone to contamination with heterotrophic bacteria.
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