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Hello,
I have some problems in using LSC to correct Pacbio reads. I would like to hybrid assemble E. coli MG1655 genome. Firstly, I use Illumina 100bp short reads data to correct Pacbio data by LSC. Then I assemble the corrected long reads with MIRA3. After correction by LSC, I align the corrected long reads against the reference genome to see whether the corrected reads cover the E. coli genome. However, I found some of the corrected reads could not complete map to the reference genome, suggesting errors in the corrected reads. On the other hand, I also take the corrected reads to do assembly with MIRA3. The output genome size is about 7Mb (not 4.6Mb), which suggests that the corrected long reads generated by LSC could not be utilized for genome assembly. I don't know whether LSC is proper to correct long reads of genomic sequence for de novo assembly, or do I make any mistake? Does anyone have the same experience or any suggestion? By the way, with the same data, I can manipulate pacBioToCA to get a reasonable genome assembly.
short reads data: http://www.illumina.com/truseq/tru_r.../datasets.ilmn
Pacbio data: https://github.com/PacificBioscience...rid%20Assembly
I have some problems in using LSC to correct Pacbio reads. I would like to hybrid assemble E. coli MG1655 genome. Firstly, I use Illumina 100bp short reads data to correct Pacbio data by LSC. Then I assemble the corrected long reads with MIRA3. After correction by LSC, I align the corrected long reads against the reference genome to see whether the corrected reads cover the E. coli genome. However, I found some of the corrected reads could not complete map to the reference genome, suggesting errors in the corrected reads. On the other hand, I also take the corrected reads to do assembly with MIRA3. The output genome size is about 7Mb (not 4.6Mb), which suggests that the corrected long reads generated by LSC could not be utilized for genome assembly. I don't know whether LSC is proper to correct long reads of genomic sequence for de novo assembly, or do I make any mistake? Does anyone have the same experience or any suggestion? By the way, with the same data, I can manipulate pacBioToCA to get a reasonable genome assembly.
short reads data: http://www.illumina.com/truseq/tru_r.../datasets.ilmn
Pacbio data: https://github.com/PacificBioscience...rid%20Assembly