Best way to merge data from two separate sequence runs
Hi,
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.
Hi,
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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