Hi all,
I have downloaded and tried to install the program Vicuna (http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/vicuna) but after major troubles with make, decided to run it from the provided executable
OMP_NUM_THREADS=2 ./vicuna-omp.static.linux64 config/vicuna_config.txt
on Illumina run with reads in R1.fastq and R2.fastq.
In the paper (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3469330/figure/F1/) and on the Broad Institutes website two optional steps are described :
1) Filtering the reads by providing a MSA of target reference genomes
2) "After initial assembly, it can also use existing genomes to perform guided merging of contigs."
While for 1) one has to write the path of the MSA file in the vicuna_config.txt at the respective line, I could not find any hint how to address or select option 2).
At least I could not spot any parameter in the configuration files vicuna_cofig.txt or vanalysis_contig.txt or in any of the src files (*cpp, *h) where a single reference genome fasta file could be requested.
I got several long contigs of a potentially novel RNA virus genome sequence, as the closest BLAST blastn hit with 75-80 % nt identity points to a ~15k long genome of similar virus species. So I would like to use this genome as scaffolding/merging template, if such an option is possible with VICUNA after all.
Does anybody have experience how to do this in VICUNA? I also looked at M-Vicuna as part of the viral-ngs suite on github but could not find anything.
Any suggestions, work-arounds, or alternatives how to finally get these contigs in one linear consensus sequence would be highly appreciated.
Thanks in advance, Katharina
