Hello everyone,
I'm new to PacBio so I need your help to guide me or give me some suggestions on my de novo assembly project. I'm currently working on a ~23mb genome and I got ~40x coverage from 3 cells. Thus we decided to use HGAP to do assembly.
When I check the official pacbio user guide https://github.com/PacificBioscience...-SMRT-Analysis
It seems strongly encourage to use their portal. However, I wanted to apply those key steps on our cluster machine, 1BLASR, 2PB/dagcon, 3CA/overlap, 4CA/unitigger, 5PB/utgcns, 6Quiver but I cant find any instruction of using command line tools in any sites. So I would like to ask that if anyone knows how to use command line tools to achieve this goal? We have newest smrtanalysis 2.3.0 in our cluster but I cant find CA/overlap and CA/unitigger under our bin, so is there any package that we need to download?
Thank you for answering my question.
JTC
I'm new to PacBio so I need your help to guide me or give me some suggestions on my de novo assembly project. I'm currently working on a ~23mb genome and I got ~40x coverage from 3 cells. Thus we decided to use HGAP to do assembly.
When I check the official pacbio user guide https://github.com/PacificBioscience...-SMRT-Analysis
It seems strongly encourage to use their portal. However, I wanted to apply those key steps on our cluster machine, 1BLASR, 2PB/dagcon, 3CA/overlap, 4CA/unitigger, 5PB/utgcns, 6Quiver but I cant find any instruction of using command line tools in any sites. So I would like to ask that if anyone knows how to use command line tools to achieve this goal? We have newest smrtanalysis 2.3.0 in our cluster but I cant find CA/overlap and CA/unitigger under our bin, so is there any package that we need to download?
Thank you for answering my question.
JTC
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