Hi, Brian,
Thanks for building this amazing assembler. I have been using it from within the Geneious software package for a few weeks now with great success. Quick question: is it possible to enter a command line under 'custom Tadpole options' that will cause the assembler to only use a specific percentage of the data? Also, is it possible to specify usage of maximum number of reads when performing the assembly (as opposed to a percent)?
I ask because I am trying to assembly a large number of plasmids from MiSeq FASTQ data, and I've found that the results are much better when only using 10% of the data. However, there is a bug wherein this option is missing from the workflow version of Tadpole; and another where it defaults to 100% when attempting to assemble each sequence list separately. They know about the first bug and are fixing it, but I thought there might be a quick workaround via the command line.
Thanks!
Rob
Thanks for building this amazing assembler. I have been using it from within the Geneious software package for a few weeks now with great success. Quick question: is it possible to enter a command line under 'custom Tadpole options' that will cause the assembler to only use a specific percentage of the data? Also, is it possible to specify usage of maximum number of reads when performing the assembly (as opposed to a percent)?
I ask because I am trying to assembly a large number of plasmids from MiSeq FASTQ data, and I've found that the results are much better when only using 10% of the data. However, there is a bug wherein this option is missing from the workflow version of Tadpole; and another where it defaults to 100% when attempting to assemble each sequence list separately. They know about the first bug and are fixing it, but I thought there might be a quick workaround via the command line.
Thanks!
Rob
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