Hi, I am new to pacbio sequencing analysis and I would really appreciate an answer to question I have about the polishing of an assembled genome assembly using QUIVER as mentioned in the Genome Assembly with Falcon in the Methods Section of the paper Paajanen et al., Scientific Data, 4:170149, 2017.
In the subsection titled "Genome assembly with FALCON" in the Methods Section, the genome polishing is described as below:
“We used QUIVER to polish the PacBio assembly using part of the SMRTANALYSIS 2.3.0p5 (pacb. com) pipeline using default settings and the combined PacBio data from 7 SMRT cells in native h5 format of PacBio. In preparation for polishing, we had to rename the scaffolds from the FALCON assembly, by concatenating the fasta names, using a custom script, called rename_falcon_github.py (github. com/paajanen/FC_scientific_data/). We uploaded both the renamed primary contigs and the renamed alternate contigs separately as a reference the polishing using referenceUploader --skipIndexUpdate -c -n "reference" -p /path/to/ working_directory -f /path/to/reference.fasta --saw = "sawriter -blt 8 -welter" --samIdx = "samtools faidx" --jobId = "Anonymous" --verbose. The polishing step was submitted with command smrtpipe.py --params=polishing_params.xml and the parameter file polishing_par- ams.xml is available at github.com/paajanen/FC_scientific_data/ “
I have used the FALCON software for genome sequencing from PacBio reads. The documentation for fc_unzip mentions that it runs quiver if the bam files of the subreads are provided.
Which is the preferred workflow - i) running fc_run followed by fc_unzip or ii) running fc_run followed by the quiver based polishing as described by Paajanen et al. ?
Also I installed smrtlinks-ttols using conda but this set of tools does not contain the referenceUploader mentioned by Paajanen et al. Where can I find this tool ?
Thanks in advance.