rhallPB
rhallPB
The raw read coverage isn't tracked through the falcon workflow, The most straightforward approach is to resequencing the raw reads against the assembly, a step required in polishing the final...
Yes, I would run the full resequencing workflow in order to generate a polished assembly. [https://github.com/PacificBiosciences/GenomicConsensus/blob/master/doc/HowTo.rst#running-a-large-scale-resequencingpolishing-job-in-smrtanalysis-23](https://github.com/PacificBiosciences/GenomicConsensus/blob/master/doc/HowTo.rst#running-a-large-scale-resequencingpolishing-job-in-smrtanalysis-23)
The parameters look reasonable, for a specific assembly the only way to really optimize for speed is to monitor the load on the computer when the assembly is running. By...
The number of jobs being created is probably too large. The `-s` option (size of the sequence blocking in daligner jobs) of the `DBsplit_option` parameters should be increased, try starting...
Questions 1,2 & 3 are all related, basically yes, cns_concurrent_jobs x --n_core (falcon_sense_option) = total_cpus. 4. Overlap filtering is a single job, and ran on a single node, there is...
Quiver / Arrow (for sequel data) would be the next step. Merge the p_ctg and a_ctg files before correction. [https://github.com/PacificBiosciences/GenomicConsensus/blob/master/doc/HowTo.rst](url) Then depending on how far you want to take the...
Resequencing in smrtportal = Quiver / Arrow. Technically quiver / arrow is the algorithm that calls consensus given an alignment, resequencing generates the alignment (using blasr) then calls consensus.
Run Falcon unzip directly after falcon, unzip uses Quiver to call consensus on the final unzipped contigs, using the phased reads, removing the need for a further round of quiver.
Yes provided you have a lot of coverage. If you don't have enough coverage then you may not end up with enough phased reads for each contig (phased haplotig) to...
Unzip and correction are experimental, I would certainly suggest using BUSCO gene completeness as a measure of sequence quality at different stages.