Thu, 11/21/2013 at 9:19 AM
Customer is a USDA researcher. He talks about difficulty filling gaps in fungal genome assembled with Ion PGM and PacBio data.
Thu, 11/21/2013 at 2:41 PM
AccuraScience LB: We would like to know some parameters for the genome and assembly, e.g., the size of the genome (fungal genomes are typically about 30MB), the current contig N50 and average contig size, and coverage is for existing sequencing data.
If the coverage is low, then you might need to perform more sequencing experiments. If there are too many contigs, we could try to re-assemble it using different software/pipelines. If both contig parameters and coverage look good, then we could try to figure out if there are better ways to fill the gaps.
The options you have may also have to do what you are looking for. If you just want to get the gene/protein's sequences, then it may not be necessary for you to get very long contigs. Gene prediction could go ahead with the shorter contigs.
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Note: LB stands for Lead Bioinformatician. An AccuraScience LB is a senior bioinformatics expert and leader of an AccuraScience data analysis team.
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